pyopenms 2.3.0__zip

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/qcML_0.0.7.xsd

@@ -0,0 +1,235 @@
+<!-- qcML version 0.0.7
+Distributed under the Creative Commons license http://creativecommons.org/licenses/by/2.0/.
+-->
+<xsd:schema xmlns="http://www.prime-xs.eu/ms/qcml" targetNamespace="http://www.prime-xs.eu/ms/qcml" xmlns:xsd="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" version="0.0.7">
+	<xsd:element name="qcML" type="qcMLType">
+		<xsd:annotation>
+			<xsd:documentation>The qcML file XML root element containing several QualityAssessments to runs and an optional QualityAssessment to the whole set</xsd:documentation>
+		</xsd:annotation>
+	</xsd:element>
+	<xsd:complexType name="qcMLType">
+		<xsd:annotation>
+			<xsd:documentation>The type of the root element</xsd:documentation>
+		</xsd:annotation>
+		<xsd:sequence>
+			<xsd:element name="runQuality" maxOccurs="unbounded">
+				<xsd:complexType>
+					<xsd:complexContent>
+						<xsd:extension base="runQualityAssessmentType">
+							<xsd:attribute name="ID" type="xsd:ID" use="required"/>
+						</xsd:extension>
+					</xsd:complexContent>
+				</xsd:complexType>
+			</xsd:element>
+			<xsd:element name="setQuality" minOccurs="0" maxOccurs="unbounded">
+				<xsd:complexType>
+					<xsd:complexContent>
+						<xsd:extension base="setQualityAssessmentType">
+							<xsd:attribute name="ID" type="xsd:ID" use="required"/>
+						</xsd:extension>
+					</xsd:complexContent>
+				</xsd:complexType>
+			</xsd:element>
+			<xsd:element name="cvList" type="cvListType">
+				<xsd:annotation>
+					<xsd:documentation>the list of cvParams referenced by the QualityParameters</xsd:documentation>
+				</xsd:annotation>
+			</xsd:element>
+		</xsd:sequence>
+	</xsd:complexType>
+	<xsd:complexType name="cvListType">
+		<xsd:annotation>
+			<xsd:documentation>The list of controlled vocabularies used in the file.</xsd:documentation>
+		</xsd:annotation>
+		<xsd:sequence>
+			<xsd:element name="cv" type="cvType" maxOccurs="unbounded">
+				<xsd:annotation>
+					<xsd:documentation>these are describing the controlled vocabularies containing the used parameters</xsd:documentation>
+				</xsd:annotation>
+			</xsd:element>
+		</xsd:sequence>
+	</xsd:complexType>
+	<xsd:complexType name="qualityAssessmentType" abstract="true">
+		<xsd:annotation>
+			<xsd:documentation>The abstract base Type for QualityParameter container</xsd:documentation>
+		</xsd:annotation>
+		<xsd:choice maxOccurs="unbounded">
+			<xsd:sequence>
+				<xsd:element name="qualityParameter" type="qualityParameterType" maxOccurs="unbounded">
+					<xsd:annotation>
+						<xsd:documentation>the value modelling a QualityParameter is a pair of keyref to a cvType and value to the actual value</xsd:documentation>
+					</xsd:annotation>
+				</xsd:element>
+			</xsd:sequence>
+			<xsd:sequence>
+				<xsd:element name="attachment" maxOccurs="unbounded">
+					<xsd:annotation>
+						<xsd:documentation>the element for the binary data of a QualityParameter reference with the MIME type as additional cvParam</xsd:documentation>
+					</xsd:annotation>
+					<xsd:complexType>
+						<xsd:complexContent>
+							<xsd:extension base="attachmentType"/>
+						</xsd:complexContent>
+					</xsd:complexType>
+				</xsd:element>
+			</xsd:sequence>
+		</xsd:choice>
+	</xsd:complexType>
+	<xsd:complexType name="runQualityAssessmentType">
+		<xsd:annotation>
+			<xsd:documentation>The derived Type for QualityParameter container of a run</xsd:documentation>
+		</xsd:annotation>
+		<xsd:complexContent>
+			<xsd:extension base="qualityAssessmentType"/>
+		</xsd:complexContent>
+	</xsd:complexType>
+	<xsd:complexType name="setQualityAssessmentType">
+		<xsd:annotation>
+			<xsd:documentation>The derived Type for QualityParameter  container of a Set</xsd:documentation>
+		</xsd:annotation>
+		<xsd:complexContent>
+			<xsd:extension base="qualityAssessmentType"/>
+		</xsd:complexContent>
+	</xsd:complexType>
+	<xsd:simpleType name="listOfStrings">
+		<xsd:list itemType="xsd:string"/>
+	</xsd:simpleType>
+	<xsd:simpleType name="listOfDoubles">
+		<xsd:list itemType="xsd:double"/>
+	</xsd:simpleType>
+	<xsd:simpleType name="listOfDoublesOrNulls">
+		<xsd:list itemType="doubleOrNullType"/>
+	</xsd:simpleType>
+	<xsd:simpleType name="doubleOrNullType">
+		<xsd:union memberTypes="xsd:double">
+			<xsd:simpleType>
+				<xsd:restriction base="xsd:token">
+					<xsd:enumeration value="null"/>
+				</xsd:restriction>
+			</xsd:simpleType>
+		</xsd:union>
+	</xsd:simpleType>
+	<xsd:simpleType name="versionRegex">
+		<xsd:restriction base="xsd:string">
+			<xsd:pattern value="(1\.1\.\d+)"/>
+		</xsd:restriction>
+	</xsd:simpleType>
+	<xsd:complexType name="abstractParamType" abstract="true">
+		<xsd:annotation>
+			<xsd:documentation>Abstract entity allowing either cvParam or userParam to be referenced in other schemas. </xsd:documentation>
+		</xsd:annotation>
+		<xsd:attribute name="name" type="xsd:string" use="required">
+			<xsd:annotation>
+				<xsd:documentation>The name of the parameter.</xsd:documentation>
+			</xsd:annotation>
+		</xsd:attribute>
+		<xsd:attribute name="value" type="xsd:string">
+			<xsd:annotation>
+				<xsd:documentation>The user-entered value of the parameter, e.g. ppm value of accuracy or the file name if CV is a mime type</xsd:documentation>
+			</xsd:annotation>
+		</xsd:attribute>
+		<xsd:attribute name="unitAccession" type="xsd:string">
+			<xsd:annotation>
+				<xsd:documentation>An accession number identifying the unit within the OBO foundry Unit CV. </xsd:documentation>
+			</xsd:annotation>
+		</xsd:attribute>
+		<xsd:attribute name="unitName" type="xsd:string">
+			<xsd:annotation>
+				<xsd:documentation>The name of the unit.</xsd:documentation>
+			</xsd:annotation>
+		</xsd:attribute>
+		<xsd:attribute name="unitCvRef" type="xsd:string">
+			<xsd:annotation>
+				<xsd:documentation>If a unit term is referenced, this attribute must refer to the CV 'id' attribute defined in the cvList in this file. </xsd:documentation>
+			</xsd:annotation>
+		</xsd:attribute>
+	</xsd:complexType>
+	<xsd:complexType name="attachmentType">
+		<xsd:annotation>
+			<xsd:documentation>A single attachment containing binary data or a table. The cvParam contains the description fitting to rhe referenced quality parameter. The MIME type is given in unit of the cv.</xsd:documentation>
+		</xsd:annotation>
+		<xsd:complexContent>
+			<xsd:extension base="cvParamType">
+				<xsd:choice>
+					<xsd:element name="binary" type="xsd:base64Binary"/>
+					<xsd:sequence>
+						<xsd:element name="tableColumnTypes" type="listOfStrings">
+							<xsd:annotation>
+								<xsd:documentation>List (space separated) of cvRefs determining the type of the respective column</xsd:documentation>
+							</xsd:annotation>
+						</xsd:element>
+						<xsd:element name="tableRowValues" type="listOfStrings" maxOccurs="unbounded"/>
+					</xsd:sequence>
+				</xsd:choice>
+				<xsd:attribute name="ID" type="xsd:ID" use="required"/>
+				<xsd:attribute name="qualityParameterRef"/>
+			</xsd:extension>
+		</xsd:complexContent>
+	</xsd:complexType>
+	<xsd:complexType name="qualityParameterType">
+		<xsd:annotation>
+			<xsd:documentation>A quality parameter contains a value and a cv, as well as a optional threshold element</xsd:documentation>
+		</xsd:annotation>
+		<xsd:complexContent>
+			<xsd:extension base="cvParamType">
+				<xsd:sequence minOccurs="0">
+					<xsd:element name="threshold" maxOccurs="unbounded">
+						<xsd:complexType>
+							<xsd:complexContent>
+								<xsd:extension base="cvParamType">
+									<xsd:attribute name="thresholdFilename" type="xsd:string"/>
+								</xsd:extension>
+							</xsd:complexContent>
+						</xsd:complexType>
+					</xsd:element>
+				</xsd:sequence>
+				<xsd:attribute name="ID" type="xsd:ID" use="required"/>
+				<xsd:attribute name="flag" type="xsd:boolean"/>
+			</xsd:extension>
+		</xsd:complexContent>
+	</xsd:complexType>
+	<xsd:complexType name="cvParamType">
+		<xsd:annotation>
+			<xsd:documentation>A single entry from an ontology or a controlled vocabulary.</xsd:documentation>
+		</xsd:annotation>
+		<xsd:complexContent>
+			<xsd:extension base="abstractParamType">
+				<xsd:attribute name="cvRef" type="xsd:IDREF" use="required">
+					<xsd:annotation>
+						<xsd:documentation>A reference to the cv element from which this term originates. </xsd:documentation>
+					</xsd:annotation>
+				</xsd:attribute>
+				<xsd:attribute name="accession" type="xsd:string" use="required">
+					<xsd:annotation>
+						<xsd:documentation>The accession or ID number of this CV term in the source CV. </xsd:documentation>
+					</xsd:annotation>
+				</xsd:attribute>
+			</xsd:extension>
+		</xsd:complexContent>
+	</xsd:complexType>
+	<xsd:complexType name="cvType">
+		<xsd:annotation>
+			<xsd:documentation>A source controlled vocabulary from which cvParams will be obtained.</xsd:documentation>
+		</xsd:annotation>
+		<xsd:attribute name="fullName" type="xsd:string" use="required">
+			<xsd:annotation>
+				<xsd:documentation>The full name of the CV.</xsd:documentation>
+			</xsd:annotation>
+		</xsd:attribute>
+		<xsd:attribute name="version" type="xsd:string">
+			<xsd:annotation>
+				<xsd:documentation>The version of the CV.</xsd:documentation>
+			</xsd:annotation>
+		</xsd:attribute>
+		<xsd:attribute name="uri" type="xsd:anyURI" use="required">
+			<xsd:annotation>
+				<xsd:documentation>The URI of the source CV.</xsd:documentation>
+			</xsd:annotation>
+		</xsd:attribute>
+		<xsd:attribute name="ID" type="xsd:ID" use="required">
+			<xsd:annotation>
+				<xsd:documentation>The unique identifier of this cv within the document to be referenced by cvParam elements. </xsd:documentation>
+			</xsd:annotation>
+		</xsd:attribute>
+	</xsd:complexType>
+</xsd:schema>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/separation_technique_1.0.xsd

@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- edited with XMLSPY v2004 rel. 3 U (http://www.xmlspy.com) by Patrick Pedrioli (Institute For Systems Biology) -->
+<xs:schema targetNamespace="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1" xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1" xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+	<xs:element name="separationTechnique" type="separationTechniqueType" abstract="true">
+		<xs:annotation>
+			<xs:documentation>Since this schema is only for MS data, the actual implementation of this element is left to another schema. See "Implementing variable content containers using an abstract element and element substitution" (http://www.xfront.com/VariableContentContainers.pdf).</xs:documentation>
+		</xs:annotation>
+	</xs:element>
+	<xs:complexType name="separationTechniqueType"/>
+</xs:schema>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/xQuest_1_0.xsd

@@ -0,0 +1,210 @@
+<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+  <xs:element name="xquest_merger">
+    <xs:complexType>
+      <xs:sequence>
+        <xs:element name="xquest_results">
+          <xs:complexType>
+            <xs:sequence>
+              <xs:element name="spectrum_search" maxOccurs="unbounded" minOccurs="0">
+                <xs:complexType mixed="true">
+                  <xs:sequence>
+                    <xs:element name="search_hit" maxOccurs="unbounded" minOccurs="0">
+                      <xs:complexType>
+                        <xs:simpleContent>
+                          <xs:extension base="xs:string">
+                            <xs:attribute type="xs:float" name="Mr" use="optional"/>
+                            <xs:attribute type="xs:float" name="TIC" use="optional"/>
+                            <xs:attribute type="xs:float" name="TIC_alpha" use="optional"/>
+                            <xs:attribute type="xs:float" name="TIC_beta" use="optional"/>
+                            <xs:attribute type="xs:string" name="annotated_spec" use="optional"/>
+                            <xs:attribute type="xs:float" name="apriori_match_probs" use="optional"/>
+                            <xs:attribute type="xs:float" name="apriori_match_probs_log" use="optional"/>
+                            <xs:attribute type="xs:string" name="backboneions_matched" use="optional"/>
+                            <xs:attribute type="xs:byte" name="charge" use="optional"/>
+                            <xs:attribute type="xs:float" name="error" use="optional"/>
+                            <xs:attribute type="xs:float" name="error_rel" use="optional"/>
+                            <xs:attribute type="xs:string" name="id" use="optional"/>
+                            <xs:attribute type="xs:float" name="intsum" use="optional"/>
+                            <xs:attribute type="xs:string" name="match_error_mean" use="optional"/>
+                            <xs:attribute type="xs:string" name="match_error_stdev" use="optional"/>
+                            <xs:attribute type="xs:float" name="match_odds" use="optional"/>
+                            <xs:attribute type="xs:float" name="match_odds_alphacommon" use="optional"/>
+                            <xs:attribute type="xs:float" name="match_odds_alphaxlink" use="optional"/>
+                            <xs:attribute type="xs:float" name="match_odds_betacommon" use="optional"/>
+                            <xs:attribute type="xs:float" name="match_odds_betaxlink" use="optional"/>
+                            <xs:attribute type="xs:float" name="measured_mass" use="optional"/>
+                            <xs:attribute type="xs:float" name="mz" use="optional"/>
+                            <xs:attribute type="xs:byte" name="num_of_matched_common_ions_alpha" use="optional"/>
+                            <xs:attribute type="xs:byte" name="num_of_matched_common_ions_beta" use="optional"/>
+                            <xs:attribute type="xs:byte" name="num_of_matched_ions_alpha" use="optional"/>
+                            <xs:attribute type="xs:byte" name="num_of_matched_ions_beta" use="optional"/>
+                            <xs:attribute type="xs:byte" name="num_of_matched_xlink_ions_alpha" use="optional"/>
+                            <xs:attribute type="xs:byte" name="num_of_matched_xlink_ions_beta" use="optional"/>
+                            <xs:attribute type="xs:float" name="prescore" use="optional"/>
+                            <xs:attribute type="xs:float" name="prescore_alpha" use="optional"/>
+                            <xs:attribute type="xs:float" name="prescore_beta" use="optional"/>
+                            <xs:attribute type="xs:string" name="prot1" use="optional"/>
+                            <xs:attribute type="xs:string" name="prot2" use="optional"/>
+                            <xs:attribute type="xs:float" name="score" use="optional"/>
+                            <xs:attribute type="xs:byte" name="search_hit_rank" use="optional"/>
+                            <xs:attribute type="xs:string" name="seq1" use="optional"/>
+                            <xs:attribute type="xs:string" name="seq2" use="optional"/>
+                            <xs:attribute type="xs:float" name="series_score_mean" use="optional"/>
+                            <xs:attribute type="xs:string" name="structure" use="optional"/>
+                            <xs:attribute type="xs:string" name="topology" use="optional"/>
+                            <xs:attribute type="xs:string" name="type" use="optional"/>
+                            <xs:attribute type="xs:float" name="wTIC" use="optional"/>
+                            <xs:attribute type="xs:float" name="weighted_matchodds_mean" use="optional"/>
+                            <xs:attribute type="xs:float" name="weighted_matchodds_sum" use="optional"/>
+                            <xs:attribute type="xs:float" name="xcorrall" use="optional"/>
+                            <xs:attribute type="xs:float" name="xcorrb" use="optional"/>
+                            <xs:attribute type="xs:float" name="xcorrx" use="optional"/>
+                            <xs:attribute type="xs:float" name="xlinkermass" use="optional"/>
+                            <xs:attribute type="xs:string" name="xlinkions_matched" use="optional"/>
+                            <xs:attribute type="xs:string" name="xlinkposition" use="optional"/>
+                          </xs:extension>
+                        </xs:simpleContent>
+                      </xs:complexType>
+                    </xs:element>
+                  </xs:sequence>
+                  <xs:attribute type="xs:float" name="Mr_precursor" use="optional"/>
+                  <xs:attribute type="xs:byte" name="addedMass" use="optional"/>
+                  <xs:attribute type="xs:float" name="apriori_pmatch_common" use="optional"/>
+                  <xs:attribute type="xs:float" name="apriori_pmatch_xlink" use="optional"/>
+                  <xs:attribute type="xs:byte" name="charge_precursor" use="optional"/>
+                  <xs:attribute type="xs:float" name="ionintensity_stdev" use="optional"/>
+                  <xs:attribute type="xs:short" name="iontag_ncandidates" use="optional"/>
+                  <xs:attribute type="xs:float" name="mean_ionintensity" use="optional"/>
+                  <xs:attribute type="xs:float" name="mz_precursor" use="optional"/>
+                  <xs:attribute type="xs:string" name="mzscans" use="optional"/>
+                  <xs:attribute type="xs:byte" name="ncommonions" use="optional"/>
+                  <xs:attribute type="xs:byte" name="nxlinkions" use="optional"/>
+                  <xs:attribute type="xs:string" name="rtsecscans" use="optional"/>
+                  <xs:attribute type="xs:string" name="scantype" use="optional"/>
+                  <xs:attribute type="xs:string" name="spectrum" use="optional"/>
+                </xs:complexType>
+              </xs:element>
+            </xs:sequence>
+            <xs:attribute type="xs:string" name="AArequired"/>
+            <xs:attribute type="xs:byte" name="CID_match2ndisotope"/>
+            <xs:attribute type="xs:float" name="Hatom"/>
+            <xs:attribute type="xs:byte" name="Iontag_charges_for_index"/>
+            <xs:attribute type="xs:short" name="Iontag_writeaftern"/>
+            <xs:attribute type="xs:byte" name="Iontagmode"/>
+            <xs:attribute type="xs:byte" name="RuntimeDecoys"/>
+            <xs:attribute type="xs:float" name="a_ion"/>
+            <xs:attribute type="xs:string" name="author"/>
+            <xs:attribute type="xs:byte" name="averageMS2"/>
+            <xs:attribute type="xs:float" name="b_ion"/>
+            <xs:attribute type="xs:float" name="c_ion"/>
+            <xs:attribute type="xs:byte" name="commonlossxcorrweigth"/>
+            <xs:attribute type="xs:byte" name="commonxcorrweigth"/>
+            <xs:attribute type="xs:byte" name="copydb2resdir"/>
+            <xs:attribute type="xs:short" name="cp_dynamic_range"/>
+            <xs:attribute type="xs:float" name="cp_isotopediff"/>
+            <xs:attribute type="xs:byte" name="cp_minpeaknumber"/>
+            <xs:attribute type="xs:byte" name="cp_nhighest"/>
+            <xs:attribute type="xs:float" name="cp_peakratio"/>
+            <xs:attribute type="xs:string" name="cp_scaleby"/>
+            <xs:attribute type="xs:byte" name="cp_scaleintensity"/>
+            <xs:attribute type="xs:byte" name="cp_threshold"/>
+            <xs:attribute type="xs:short" name="cp_tolerance"/>
+            <xs:attribute type="xs:string" name="cp_tolerancemeasure"/>
+            <xs:attribute type="xs:short" name="cp_tolerancexl"/>
+            <xs:attribute type="xs:string" name="crosslinkername"/>
+            <xs:attribute type="xs:string" name="database"/>
+            <xs:attribute type="xs:string" name="database_dc"/>
+            <xs:attribute type="xs:string" name="date"/>
+            <xs:attribute type="xs:string" name="deffile"/>
+            <xs:attribute type="xs:byte" name="drawlogscale"/>
+            <xs:attribute type="xs:byte" name="drawspectra"/>
+            <xs:attribute type="xs:byte" name="enumerate"/>
+            <xs:attribute type="xs:string" name="enumeration_index_mode"/>
+            <xs:attribute type="xs:byte" name="enzyme_num"/>
+            <xs:attribute type="xs:string" name="experiment"/>
+            <xs:attribute type="xs:string" name="fragmentresiduals"/>
+            <xs:attribute type="xs:string" name="fwd_ions"/>
+            <xs:attribute type="xs:anyURI" name="homepage"/>
+            <xs:attribute type="xs:string" name="indexcharges_common"/>
+            <xs:attribute type="xs:byte" name="intprecision"/>
+            <xs:attribute type="xs:float" name="intsumweight"/>
+            <xs:attribute type="xs:string" name="ioncharge_common"/>
+            <xs:attribute type="xs:string" name="ioncharge_xlink"/>
+            <xs:attribute type="xs:byte" name="ionindexintprecision"/>
+            <xs:attribute type="xs:string" name="ionseries"/>
+            <xs:attribute type="xs:string" name="ionseries_array"/>
+            <xs:attribute type="xs:byte" name="iontag_match_xlinkions"/>
+            <xs:attribute type="xs:float" name="matchoddsweight"/>
+            <xs:attribute type="xs:byte" name="maxdigestlength"/>
+            <xs:attribute type="xs:short" name="maxionsize"/>
+            <xs:attribute type="xs:byte" name="maxiontaghits"/>
+            <xs:attribute type="xs:short" name="maxpepmr"/>
+            <xs:attribute type="xs:byte" name="mindigestlength"/>
+            <xs:attribute type="xs:byte" name="minhits"/>
+            <xs:attribute type="xs:byte" name="minionintensity"/>
+            <xs:attribute type="xs:short" name="minionsize"/>
+            <xs:attribute type="xs:byte" name="miniontaghits"/>
+            <xs:attribute type="xs:short" name="minpepmr"/>
+            <xs:attribute type="xs:byte" name="missed_cleavages"/>
+            <xs:attribute type="xs:string" name="monolinkmw"/>
+            <xs:attribute type="xs:byte" name="ms1tol_maxborder"/>
+            <xs:attribute type="xs:byte" name="ms1tol_minborder"/>
+            <xs:attribute type="xs:byte" name="ms1tolerance"/>
+            <xs:attribute type="xs:float" name="ms2tolerance"/>
+            <xs:attribute type="xs:byte" name="nh3loss"/>
+            <xs:attribute type="xs:byte" name="nocutatxlink"/>
+            <xs:attribute type="xs:byte" name="normxcorr"/>
+            <xs:attribute type="xs:byte" name="ntermxlinkable"/>
+            <xs:attribute type="xs:byte" name="ntestions"/>
+            <xs:attribute type="xs:byte" name="nvariable_mod"/>
+            <xs:attribute type="xs:string" name="outputpath"/>
+            <xs:attribute type="xs:short" name="picktolerance"/>
+            <xs:attribute type="xs:string" name="picktolerance_measure"/>
+            <xs:attribute type="xs:byte" name="poolisotopes"/>
+            <xs:attribute type="xs:byte" name="printcandidatepeps"/>
+            <xs:attribute type="xs:byte" name="printdigestpeps"/>
+            <xs:attribute type="xs:byte" name="printpeptides"/>
+            <xs:attribute type="xs:byte" name="printtables"/>
+            <xs:attribute type="xs:byte" name="realintensities4xcorr"/>
+            <xs:attribute type="xs:byte" name="redundant_peps"/>
+            <xs:attribute type="xs:byte" name="reportnbesthits"/>
+            <xs:attribute type="xs:byte" name="requiredmissed_cleavages"/>
+            <xs:attribute type="xs:string" name="rev_ions"/>
+            <xs:attribute type="xs:byte" name="search_intercrosslinks"/>
+            <xs:attribute type="xs:byte" name="search_intracrosslinks"/>
+            <xs:attribute type="xs:byte" name="search_intralinks"/>
+            <xs:attribute type="xs:short" name="search_maxcandidate_peps"/>
+            <xs:attribute type="xs:byte" name="search_monolinks"/>
+            <xs:attribute type="xs:string" name="testionspick"/>
+            <xs:attribute type="xs:string" name="tolerancemeasure"/>
+            <xs:attribute type="xs:string" name="tolerancemeasure_ms2"/>
+            <xs:attribute type="xs:byte" name="tryptic_termini"/>
+            <xs:attribute type="xs:byte" name="uselossionsformatching"/>
+            <xs:attribute type="xs:byte" name="usenprescores"/>
+            <xs:attribute type="xs:string" name="variable_mod"/>
+            <xs:attribute type="xs:byte" name="verbose"/>
+            <xs:attribute type="xs:float" name="wTICweight"/>
+            <xs:attribute type="xs:byte" name="waterloss"/>
+            <xs:attribute type="xs:int" name="writetodiskaftern"/>
+            <xs:attribute type="xs:float" name="x_ion"/>
+            <xs:attribute type="xs:byte" name="xcorr_tolerance_window"/>
+            <xs:attribute type="xs:float" name="xcorrbweight"/>
+            <xs:attribute type="xs:byte" name="xcorrdelay"/>
+            <xs:attribute type="xs:float" name="xcorrprecision"/>
+            <xs:attribute type="xs:float" name="xcorrxweight"/>
+            <xs:attribute type="xs:string" name="xkinkerID"/>
+            <xs:attribute type="xs:float" name="xlink_ms2tolerance"/>
+            <xs:attribute type="xs:float" name="xlinkermw"/>
+            <xs:attribute type="xs:short" name="xlinktypes"/>
+            <xs:attribute type="xs:byte" name="xlinkxcorrweigth"/>
+            <xs:attribute type="xs:string" name="xquest_version"/>
+            <xs:attribute type="xs:float" name="y_ion"/>
+            <xs:attribute type="xs:float" name="z_ion"/>
+          </xs:complexType>
+        </xs:element>
+      </xs:sequence>
+      <xs:attribute type="xs:string" name="inputfiles"/>
+      <xs:attribute type="xs:float" name="version"/>
+    </xs:complexType>
+  </xs:element>
+</xs:schema>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/InternalCalibration_Models.R

@@ -0,0 +1,40 @@
+library("ggplot2")
+library("reshape2")
+
+file.table.in = commandArgs(TRUE)[1] ## file.table.in = "models.csv"
+file.plot.out = commandArgs(TRUE)[2] ## file.plot.out = "output.png"
+
+cat(paste0("Reading file '", file.table.in, "' to plot model parameters ..."))
+
+d = read.csv(file.table.in, check.names = FALSE, comment.char = "#", strip.white = TRUE)
+model_count = sum(d$source == "local")
+
+dm = melt(d, id.vars = c("RT", "source"))
+head(dm)
+
+## for linear models: remove 'power' graph (it's all 0)
+if (all(dm$value[grep("power", dm$variable)] == 0, na.rm=TRUE))
+{
+  dm = dm[grep("power", dm$variable, invert=TRUE), ]
+}
+
+#options(device = "pdf")
+#dev.new(filename = file.plot.out, file = file.plot.out)
+png(filename = file.plot.out, width=1920)
+if (model_count == 0)
+{
+  plot(c(0, 1), c(0, 1), ann = F, bty = 'n', type = 'n', xaxt = 'n', yaxt = 'n')
+  text(0.5,0.5,"Model fitting failed!\nCheck your tool parameters and/or data!")
+} else {
+  pl = ggplot(dm) + 
+        geom_point(aes(x=RT, y=value, col=source)) +
+        ggtitle(paste("Model coefficients over time\n", model_count, "model(s)", collapse="")) +
+        xlab("RT [sec]") +
+        ylab("model coefficient") +
+        facet_grid(  variable ~ ., scales="free_y")
+  print(pl)
+}
+
+dev.off()
+
+

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/InternalCalibration_Residuals.R

@@ -0,0 +1,57 @@
+library("ggplot2")
+library("reshape2")
+library("plyr")
+
+file.table.in = commandArgs(TRUE)[1] ## file.table.in = "residuals.csv"
+file.plot.out = commandArgs(TRUE)[2] ## file.plot.out = "residuals.png"
+
+cat(paste0("Reading file '", file.table.in, "' to plot residual masses ..."))
+
+d = read.csv(file.table.in, comment.char = "#", strip.white = TRUE, fill = FALSE)
+head(d)
+
+## check if header is complete
+required_cols = c("RT", "intensity", "mz.ref", "mz.before", "mz.after", "ppm.before", "ppm.after")
+if (!all(required_cols %in% colnames(d))) {
+  stop(paste0("File '", file.table.in, "' has missing columns. Required are: ", paste(required_cols, sep="", collapse=", "), "."))  
+}
+
+dpm = melt(d[, grep("^mz.[ab]", colnames(d), invert = TRUE)], id.vars = c("RT", "mz.ref", "intensity"))
+head(dpm)
+## for peptide ID data, mz.ref will be mostly unique
+if (length(unique(d$mz.ref)) / nrow(d) > 0.5) {
+  dpm2 = dpm
+  dpm2$masstrace = ""
+} else {
+  ## for direct-injection, every spectrum will repeatedly give multiple 'mz.ref'
+  ## annotate mz.ref with average intensity
+  dpm2 = ddply(dpm, "mz.ref", function(x) {
+    x$masstrace = paste0("m/z ",
+                         # we want zero/space padded masses, such that ggplot will sort them by mass automatically
+                         format(round(x$mz.ref, 5), nsmall = 5, width = 9, zero.print = TRUE),
+                         " ~ int ",
+                         format(median(x$intensity), scientific = TRUE, digits = 2))
+    return(x)
+  })
+}
+head(dpm2)
+
+#getOption("device") ## RStudioGD
+#options(device = "pdf")
+#dev.new(filename = file.plot.out, file = file.plot.out)
+png(filename = file.plot.out, width=1920)
+
+pl = ggplot(dpm2) + 
+       geom_hline(yintercept = 0, colour="grey") +
+       geom_hline(yintercept = c(-1,1), colour = "grey", linetype = "dotdash") +
+       facet_wrap(~ masstrace) + 
+       geom_point(aes(x = RT, y = value, color = variable), alpha=0.6) +
+       scale_color_manual(values = c("ppm.before" = "#FF2222", "ppm.after" = "#2222FF"),
+                          labels = c("before", "after"),
+                          name = "error") +
+       ggtitle("Calibrant's mass error over time") +
+       xlab("RT [sec]") +
+       ylab("mass error [ppm]")
+print(pl)
+
+dev.off()

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_acc.R

@@ -0,0 +1,28 @@
+library("ggplot2")
+library(scales)
+options(warn=-1) #suppress warnings
+
+#options
+options(digits=10)
+
+file<-commandArgs(TRUE)[1]
+post<-commandArgs(TRUE)[2]
+#file<-"/tmp/TOPPAS_out/023-QCExtractor-out_csv/old1.csv"
+knime.in<-read.csv(file=file,head=TRUE,sep="\t")
+names(knime.in)<- c("RT", "MZ", "Score", "PeptideSequence", "Charge", "TheoreticalWeight", "DeltaPpm")
+
+png(post)
+##########################
+###Mass accuracy
+##########################
+ggplot(knime.in, aes(x=DeltaPpm)) + 
+  geom_histogram(aes(y=..density..),      # Histogram with density instead of count on y-axis
+                 binwidth=.5,
+                 colour="black", fill="white") +
+  geom_density(alpha=.1, fill="green") + # Overlay with transparent density plot
+  geom_vline(aes(xintercept=median(DeltaPpm, na.rm=T)),   # Ignore NA values for mean
+             color="red", linetype="dashed", size=1) + 
+  xlim(c(-10,10)) + 
+  ylab("Density")
+######################################
+garbage<-dev.off()

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_idmap.R

@@ -0,0 +1,39 @@
+## This is an R script to produce the figures that are attached to the qcML format
+library("ggplot2")
+library(scales)
+options(warn=-1) #suppress warnings
+
+#options
+options(digits=10)
+
+file_p<-commandArgs(TRUE)[1]
+file_id<-commandArgs(TRUE)[2]
+post<-commandArgs(TRUE)[3]
+png(post)
+#file_p<-"/tmp/TOPPAS_out/024-QCExtractor-out_csv/old1.csv"
+#file_id<-"/tmp/TOPPAS_out/023-QCExtractor-out_csv/old1.csv"
+#precs<-read.table(file_p, header=TRUE, sep="", na.strings="NA", dec=".", strip.white=TRUE)
+#ids<-read.table(file_id, header=TRUE, sep="", na.strings="NA", dec=".", strip.white=TRUE)
+precs<-read.csv(file=file_p,head=TRUE,sep="\t")
+ids<-read.csv(file=file_id,head=TRUE,sep="\t")
+names(precs)<- c("RT", "MZ")
+names(ids)<- c("RT", "MZ", "Score", "PeptideSequence", "Charge", "TheoreticalWeight", "DeltaPpm")
+
+##########################
+###IDs on rt/mz map vs precursors
+##########################
+
+spec<-cbind(precs[])
+id<-cbind(ids[,1:2])
+spec$color<-"is_recorded"
+id$color<-"is_identified"
+spec$rt<-as.POSIXct(as.character(0),format="%S")+spec$RT
+id$rt<-as.POSIXct(as.character(0),format="%S")+id$RT
+
+ggplot(spec, aes(rt, MZ, color=color)) + 
+  geom_point() + 
+  geom_point(data=id, aes(rt, MZ, color=color)) +
+  xlab("RT (HH:MM)") 
+######################################
+garbage<-dev.off()
+