pyopenms 2.3.0__zip

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_idmap.ttd

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+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>Rscript_qcfigures_idmap</type>
+		<external>
+				<text>
+					<onstartup>Calling Rscript id map ...</onstartup>
+					<onfail>Something went wrong. Is 'R' in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>FileConversion</e_category>
+			<cloptions> --vanilla "%1/ProduceQCFigures_idmap.R" "%2" "%3" "%4"</cloptions>
+			<path>Rscript</path>
+			<mappings>
+				<mapping id="1" cl="%%scriptpath" />
+				<mapping id="2" cl="%%inTSVprec" />
+				<mapping id="3" cl="%%inTSVacc" />
+				<mapping id="4" cl="%TMP/%BASENAME[%%inTSVprec]_idmap.png" />
+				<file_post location="%TMP/%BASENAME[%%inTSVprec]_idmap.png" target="out" />
+			</mappings>
+			<ini_param>
+				<ITEM name="scriptpath" value="." type="string" description="input script path, this should point
+to share/OpenMS/SCRIPTS of your OpenMS installation"/>
+				<ITEM name="inTSVprec" value="" type="string" description="tabular input data for precursor stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="inTSVacc" value="" type="string" description="tabular input data for accuracy stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="out" value="" type="string" description="output figure from R(valid formats:
+&apos;png&apos;)" tags="output file" />
+			</ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_rt_acc.ttd

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+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>Rscript_qcfigures_rt_acc</type>
+		<external>
+				<text>
+					<onstartup>Calling Rscript rt acc ...</onstartup>
+					<onfail>Something went wrong. Is 'R' in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>FileConversion</e_category>
+			<cloptions>--vanilla "%1/ProduceQCFigures_rt_acc.R" "%2" "%3"</cloptions>
+			<path>Rscript</path>
+			<mappings>
+				<mapping id="1" cl="%%scriptpath" />
+				<mapping id="2" cl="%%inTSVacc" />
+				<mapping id="3" cl="%TMP/%BASENAME[%%inTSVacc]_acc_time.png" />
+				<file_post location="%TMP/%BASENAME[%%inTSVacc]_acc_time.png" target="out" />
+			</mappings>
+			<ini_param>
+				<ITEM name="scriptpath" value="." type="string" description="input script path, this should point
+to share/OpenMS/SCRIPTS of your OpenMS installation"/>
+				<ITEM name="inTSVacc" value="" type="string" description="tabular input data for accuracy stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="out" value="" type="string" description="output figure from R(valid formats:
+&apos;png&apos;)" tags="output file" />
+			</ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_setid.ttd

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+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>Rscript_qcfigures_setid</type>
+		<external>
+				<text>
+					<onstartup>Calling Rscript set id ...</onstartup>
+					<onfail>Something went wrong. Is 'R' in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>FileConversion</e_category>
+			<cloptions>--vanilla "%1/ProduceQCFigures_setid.R" "%2" "%3"</cloptions>
+			<path>Rscript</path>
+			<mappings>
+				<mapping id="1" cl="%%scriptpath" />
+				<mapping id="2" cl="%%inTSVsetid" />
+				<mapping id="3" cl="%TMP/%BASENAME[%%inTSVsetid]_setid.png" />
+				<file_post location="%TMP/%BASENAME[%%inTSVsetid]_setid.png" target="out" />
+			</mappings>
+			<ini_param>
+				<ITEM name="scriptpath" value="." type="string" description="input script path, this should point
+to share/OpenMS/SCRIPTS of your OpenMS installation"/>
+				<ITEM name="inTSVsetid" value="" type="string" description="tabular input data for set id quantile data(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="out" value="" type="string" description="output figure from R(valid formats:
+&apos;png&apos;)" tags="output file" />
+			</ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_tic.ttd

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+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>Rscript_qcfigures_tic</type>
+		<external>
+				<text>
+					<onstartup>Calling Rscript tic ...</onstartup>
+					<onfail>Something went wrong. Is 'R' in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>FileConversion</e_category>
+			<cloptions>--vanilla "%1/ProduceQCFigures_tic.R" "%2" "%3"</cloptions>
+			<path>Rscript</path>
+			<mappings>
+				<mapping id="1" cl="%%scriptpath" />
+				<mapping id="2" cl="%%inTSVtic" />
+				<mapping id="3" cl="%TMP/%BASENAME[%%inTSVtic]_tic.png" />
+				<file_post location="%TMP/%BASENAME[%%inTSVtic]_tic.png" target="out" />
+			</mappings>
+			<ini_param>
+				<ITEM name="scriptpath" value="." type="string" description="input script path, this should point
+to share/OpenMS/SCRIPTS of your OpenMS installation"/>
+				<ITEM name="inTSVtic" value="" type="string" description="tabular input data for tic stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="out" value="" type="string" description="output figure from R(valid formats:
+&apos;png&apos;)" tags="output file" />
+			</ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_trapfill.ttd

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+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>Rscript_qcfigures_inj</type>
+		<external>
+				<text>
+					<onstartup>Calling Rscript inj ...</onstartup>
+					<onfail>Something went wrong. Is 'R' in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>FileConversion</e_category>
+			<cloptions>--vanilla "%1/ProduceQCFigures_inj.R" "%2" "%3"</cloptions>
+			<path>Rscript</path>
+			<mappings>
+				<mapping id="1" cl="%%scriptpath" />
+				<mapping id="2" cl="%%inTSVfill" />
+				<mapping id="3" cl="%TMP/%BASENAME[%%inTSVfill]_inj.png" />
+				<file_post location="%TMP/%BASENAME[%%inTSVfill]_inj.png" target="out" />
+			</mappings>
+			<ini_param>
+				<ITEM name="scriptpath" value="." type="string" description="input script path, this should point
+to share/OpenMS/SCRIPTS of your OpenMS installation"/>
+				<ITEM name="inTSVfill" value="" type="string" description="tabular input data for trap filltimes(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="out" value="" type="string" description="output figure from R(valid formats:
+&apos;png&apos;)" tags="output file" />
+			</ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/TEMPLATE.ttd_

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+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<!-- this is the name of the '-type' which is added to GenericWrapper - so chose carefully -->
+		<type>RAWFileConvert</type>
+		<!-- description of the wrapper -->
+		<external>
+      <text>
+        <onstartup>This is printed on startup ... Wrapper was tested with "external_tool" vX.Y.Z, report issues to the OpenMS team at www.OpenMS.de</onstartup>
+        <onfail>This is printed in case of error - you can list possible causes for failure here...</onfail>
+        <onfinish>This is printed when finished successfully.</onfinish>
+      </text>    
+		  <!-- currently disregarded by TOPPAS, but might become useful -->
+		  <e_category>FileConversion</e_category>
+		  <!-- command line options of your external tool (use placeholders ,e.g. %1 to insert dynamic content)
+           You should quote placeholders which hold single files, but avoid quotes for lists (ITEMLIST in ini_param section), since they are quoted by GenericWrapper
+           automatically -->
+		  <cloptions>-o "%1" --mzML "%2"</cloptions>
+		  <!-- the actual executable (usually it should be in your PATH, to avoid having to specify a full path to it) -->
+		  <path>msconvert</path>
+      <!-- sets the working directory to this path before calling the external tool. Some tools write to the current working directory
+           and thus starting the tool from somewhere else might actually lead to trouble
+           use only real paths here (no placeholders like %TMP) -->
+      <workingdirectory>.</workingdirectory>
+		  <!-- these mappings connect input parameters (from the 'ini_param' section below) and the command line options of your tool
+		       any INI parameter can be referenced using %%'param_name', e.g. %%in
+		       additionally you can use %TMP and %BASENAME[X] to get the current temp directory to store data, or the basename of X -->
+		  <mappings>
+			<mapping id="1" cl="%TMP" />
+			<mapping id="2" cl="%%in" />
+
+			<!-- input mapping/copying: this is a little hard to explain and usually you will not need it (delete all file-tags of the parameter!)
+			     what it does: when the wrapped tool works with in-place files (i.e. overwrites its input), you must copy it before invoking the tool,
+			                   e.g. TPP's RefreshParser will overwrite its input pepXML file
+			                   The targeted parameter gets replaced with a temporary filename after the copy is done, so that subsequent
+			                   operations target the temp file -->
+      <file_pre location="%TMP/%RND_%%in" target="in" />
+      
+			<!-- output mapping/moving: this is a little hard to explain and usually you will not need it (delete all file-tags of the parameter!)
+			     what it does: when you cannot specify an explicit output file to the external tool and it rather determines that by itself,
+			                   e.g. msconvert will create an output file (call it F) which has the same name as the input file with a replaced suffix
+			                   then you might need to move F to the name specified in 'out' (or any other parameter)
+			                   Thus you specify the name of F and the name of the target parameter (in terms of INI parameter values) -->
+			<file_post location="%TMP/%BASENAME[%%in].mzML" target="out" />
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="input file in RAW format(valid formats: &apos;RAW&apos;)" tags="input file" />
+			<ITEM name="out" value="" type="string" description="output file in mzML format(valid formats: &apos;mzML&apos;)" tags="output file" />
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/TPP_RefreshParser.ttd

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+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>TPP_RefreshParser</type>
+		<external>
+      <text>
+        <onstartup>Calling TPP's RefreshParser ...  Wrapper tested with TPP v4.4.1 (VUVUZELA), report issues to the OpenMS team at www.OpenMS.de</onstartup>
+        <onfail>Something went wrong. Is 'RefreshParser' in your PATH?</onfail>
+        <onfinish>Tool finished successfully.</onfinish>
+      </text>    
+		  <e_category>FileConversion</e_category>
+		  <cloptions>"%1" "%2"</cloptions>
+		  <path>RefreshParser</path>
+      <workingdirectory>.</workingdirectory>
+		  <mappings>
+			<mapping id="1" cl="%%in" />
+			<mapping id="2" cl="%%database" />
+      <file_pre location="%TMP/%RND_%BASENAME[%%in]" target="in" />
+			<file_post location="%%in" target="out" />
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="input file in pepXML format(valid formats: &apos;pepXML&apos;)" tags="input file,required" />
+      <ITEM name="database" value="" type="string" description="FASTA database to find matching proteins." tags="input file,required" />
+			<ITEM name="out" value="" type="string" description="output file in pepXML format(valid formats: &apos;pepXML&apos;)" tags="output file,required" />
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/WINDOWS/TPP_ProteinProphet.ttd

@@ -0,0 +1,46 @@
+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>TPP_ProteinProphet</type>
+		<external>
+      <text>
+        <onstartup>Calling TPP's ProteinProphet... Wrapper tested with TPP v4.4.1 (VUVUZELA), report issues to the OpenMS team at www.OpenMS.de</onstartup>
+        <onfail>Something went wrong. Possible cause: You forgot to call TPP's 'RefreshParser' prior to calling this?</onfail>
+        <onfinish>Tool finished successfully.</onfinish>
+      </text>
+		  <e_category>Protein/Peptide Identification</e_category>
+		  <cloptions>"%1" %2 EXCELPEPS %4 %6 %7 %8 %9 %10 %11</cloptions>
+		  <path>ProteinProphet</path>
+      <workingdirectory>c:/Inetpub/wwwroot/ISB</workingdirectory>
+		  <mappings>
+			<mapping id="1" cl="%%in" />
+			<mapping id="2" cl="MINPROB %%min_prob" />
+			<mapping id="4" cl="EXCEL%%excel_minprob" />
+			<mapping id="6" cl="%%flag_delude" />
+			<mapping id="7" cl="%%flag_normprotlen" />
+			<mapping id="8" cl="%%flag_logprobs" />
+			<mapping id="9" cl="%%flag_confem" />
+			<mapping id="10" cl="%%flag_allpeps" />
+			<mapping id="11" cl="%%flag_noplot" />
+			<file_post location="%WORKINGDIR/0.prot.xml" target="out" />
+			<file_post location="%WORKINGDIR/0.prot.xls" target="out_xls" />
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="Input file in pepXML format(valid formats: &apos;pepXML&apos;)" tags="input file,required" />
+			<ITEM name="out" value="" type="string" description="Output file in protXML format(valid formats: &apos;protXML&apos;)" tags="output file" />
+			<ITEM name="out_xls" value="" type="string" description="Output file in XLS format(valid formats: &apos;xls&apos;)." tags="output file" />
+
+			<ITEM name="min_prob" value="0.05" type="float" description="PeptideProphet (or any other) probabilty threshold"/>
+			<ITEM name="excel_minprob" value="0.0" type="float" description="Write output tab delim xls file including all protein (group)s with minimum probability (only meaningful when 'flag_excel' is set)." restrictions="0:1" tags=""/>
+
+			<ITEM name="flag_occam" value="" type="string" description="Do not use Occam's Razor to derive the simplest protein list to explain observed peptides" tags="" restrictions=",NOOCCAM" />
+			<ITEM name="flag_delude" value="" type="string" description="Do NOT use peptide degeneracy information when assessing proteins" tags="" restrictions=",DELUDE" />
+			<ITEM name="flag_normprotlen" value="" type="string" description="Normalize NSP using protein length" tags="" restrictions=",NORMPROTLEN" />
+			<ITEM name="flag_logprobs" value="" type="string" description="Use the log of the probabilities in the confidence calculations" tags="" restrictions=",LOGPROBS" />
+			<ITEM name="flag_confem" value="" type="string" description="Use the EM to compute probability given the confidence" tags="" restrictions=",CONFEM" />
+			<ITEM name="flag_allpeps" value="" type="string" description="Consider all possible peptides in the database in the confidence model" tags="" restrictions=",ALLPEPS" />
+			<ITEM name="flag_noplot" value="" type="string" description="do not generate plot png file" tags="" restrictions=",NOPLOT" />
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/XTandemToPercolator.ttd

@@ -0,0 +1,30 @@
+<ttd>
+	<tool status="external">
+		<category>Identification</category>
+		<type>XTandemToPercolator</type>
+		<external>
+      <text>
+        <onstartup>Running "tandem2pin" converter...</onstartup>
+        <onfail>Something went wrong. Is the tandem2pin executable globally accessible?</onfail>
+        <onfinish>tandem2pin finished successfully.</onfinish>
+      </text>    
+		  <e_category>Identification</e_category>
+		  <cloptions>--pattern "%4" --outputTab "%3" "%1" "%2"</cloptions>
+		  <path>tandem2pin</path>
+		  <workingdirectory>.</workingdirectory>
+		  <mappings>
+			<mapping id="1" cl="%%in" />
+			<mapping id="2" cl="%%in_decoy" />
+			<mapping id="3" cl="%%out" />
+            <mapping id="4" cl="%%decoy_pattern" />
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="Input file: X! Tandem search results; either from a combined target/decoy search (then set 'decoy_pattern') or from a target-only search (then set 'in_decoy') (valid formats: 'xml')" tags="input file" />
+			<ITEM name="in_decoy" value="" type="string" description="Input file: X! Tandem search results; from a decoy-only search (valid formats: 'xml')" tags="input file" />
+			<ITEM name="out" value="" type="string" description="Output file: Percolator tab-delimited input (valid formats: 'csv')" tags="output file" />
+            <ITEM name="decoy_pattern" value="DECOY_" type="string" description="Pattern identifying decoy matches. Ignored if 'in_decoy' is set, but must not be empty!" />
+            <ITEM name="enzyme" value="trypsin" type="string" description="Enzyme used for digestion" restrictions="no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin" />
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/msconvert.ttd

@@ -0,0 +1,25 @@
+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>RAWFileConvert</type>
+		<external>
+      <text>
+        <onstartup>Calling PWiz' msconvert ...</onstartup>
+        <onfail>Something went wrong. Is 'msconvert' in your PATH?</onfail>
+        <onfinish>Tool finished successfully.</onfinish>
+      </text>    
+		  <e_category>FileConversion</e_category>
+		  <cloptions>-o "%1" --mzML "%2"</cloptions>
+		  <path>msconvert</path>
+		  <mappings>
+			<mapping id="1" cl="%TMP/GenericWrapper_%RND" />
+			<mapping id="2" cl="%%in" />
+			<file_post location="%1/%BASENAME[%%in].mzML" target="out" />
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="input file in RAW format(valid formats: &apos;RAW&apos;)" tags="input file" />
+			<ITEM name="out" value="" type="string" description="output file in mzML format(valid formats: &apos;mzML&apos;)" tags="output file" />
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/XSL/APML_to_CSV.xsl

@@ -0,0 +1,43 @@
+<?xml version="1.0" ?>
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
+<xsl:output method="html"/>
+
+
+
+ <xsl:template match="/">
+     <html> 
+		 <body>
+			<xsl:apply-templates select="apml/dataProcessing/software" />
+		 <br/>
+		 #Format: RT mz Intensity Charge Mass<br/>
+       <xsl:apply-templates select="apml/data/peak_lists/peak_list/features/feature">
+ 				<xsl:sort select="@id" />
+       </xsl:apply-templates>
+		 </body>
+     </html> 
+ </xsl:template>
+
+  <xsl:template match="feature">
+		<!--<xsl:value-of select="@id" />-->
+		<xsl:apply-templates select="coordinate" />
+
+  </xsl:template>
+
+  <xsl:template match="coordinate">
+    <xsl:value-of select="@rt" /><xsl:text> </xsl:text>
+    <xsl:value-of select="@mz" /><xsl:text> </xsl:text>
+    <xsl:value-of select="@intensity" /><xsl:text> </xsl:text>
+    <xsl:value-of select="@charge" /><xsl:text> </xsl:text>
+    <xsl:value-of select="@mass" /><br/>
+  </xsl:template>
+
+		 <xsl:template match="software">
+			<xsl:text>#</xsl:text>
+		 	<xsl:value-of select="@name" /><xsl:text> (</xsl:text>
+		 	<xsl:value-of select="@version" /><xsl:text>) - </xsl:text>
+		 	<xsl:value-of select="@type" />
+	</xsl:template>
+
+
+
+</xsl:stylesheet>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/XSL/ConsensusXML.xsl

@@ -0,0 +1,76 @@
+<?xml version="1.0"	encoding="utf-8"?>
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
+	<xsl:template match="consensusXML">
+	  <html> 
+	  <body>  
+		  <xsl:apply-templates select="mapList"/>
+		  <br/>
+		  <b>Consensus elements:</b>
+		  <table border="1" align="center" style="border-style:solid; border-collapse:collapse;" width="100%" cellpadding="2">
+				<tr>
+					<th><nobr></nobr></th>
+					<th><nobr>RT</nobr></th>
+					<th><nobr>MZ</nobr></th>
+					<th><nobr>Intensity</nobr></th>
+					<th><nobr>Quality</nobr></th>
+					<th><nobr>Map Id</nobr></th>
+					<th><nobr>Element Id</nobr></th>
+				</tr>
+		  	<xsl:apply-templates select="consensusElementList/consensusElement"/>
+		  </table>
+	  </body> 
+	  </html>  
+	</xsl:template>
+	
+	<xsl:template match="mapList">
+		<b>Source map list:</b>
+		<table border="1" style="border-style:solid; border-collapse:collapse;" cellpadding="2">
+			<tr>
+				<th><nobr>Map Id</nobr></th>
+				<th><nobr>File name</nobr></th>
+				<th><nobr>Label</nobr></th>
+				<th><nobr>Size</nobr></th>
+			</tr>
+		  <xsl:apply-templates select="map"/>
+		</table>
+	</xsl:template>
+	
+	<xsl:template match="map">
+		<tr>
+			<td align="center"><xsl:value-of select="@id"/></td>
+			<td align="center"><xsl:value-of select="@name"/></td>
+			<td align="center"><xsl:value-of select="@label"/></td>
+			<td align="center"><xsl:value-of select="@size"/></td>
+		</tr>
+	</xsl:template>
+	
+	<xsl:template match="consensusElement">
+		<tr>
+			<td align="center"><b><nobr>Consensus element <xsl:value-of select="position()"/></nobr></b></td>
+			<td align="center"><b><xsl:value-of select="centroid/@rt"/></b></td>
+			<td align="center"><b><xsl:value-of select="centroid/@mz"/></b></td>
+			<td align="center"><b><xsl:value-of select="centroid/@it"/></b></td>
+			<td align="center"><b><xsl:value-of select="@quality"/></b></td>
+			<td align="center"><b></b></td>
+			<td align="center"><b></b></td>
+		</tr>
+		<xsl:apply-templates select="groupedElementList/element">
+			<xsl:sort select="@map" data-type="number" order="ascending"/>
+		</xsl:apply-templates>
+	</xsl:template>
+
+	<xsl:template match="element">
+		<tr>
+			<td align="center"></td>
+			<td align="center"><xsl:value-of select="@rt"/></td>
+			<td align="center"><xsl:value-of select="@mz"/></td>
+			<td align="center"><xsl:value-of select="@it"/></td>
+			<td align="center"></td>
+			<td align="center"><xsl:value-of select="@map"/></td>
+			<td align="center"><xsl:value-of select="@id"/></td>
+		</tr>
+	</xsl:template>
+
+</xsl:stylesheet>
+
+