| Previous changeset 1:a85c8de9630a (2015-03-26) Next changeset 3:86fd1757f102 (2015-12-21) |
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Commit message:
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty |
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modified:
gff3_to_fasta.xml protxml_to_gff.xml tool_dependencies.xml |
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added:
mzid_to_protxml.xml test-data/PeptideShaker_tiny.mzid |
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removed:
repository_dependencies.xml |
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| diff -r a85c8de9630a -r 68d8c9e521d7 gff3_to_fasta.xml --- a/gff3_to_fasta.xml Thu Mar 26 20:16:00 2015 -0400 +++ b/gff3_to_fasta.xml Tue Oct 20 20:34:50 2015 -0400 |
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| @@ -1,40 +1,29 @@ -<tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.0"> - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> +<tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.1"> + <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> </requirements> - - <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description> - - <command> - augustus_to_proteindb.rb $gff_file -o $output $coords - </command> - - - - - <stdio> - <exit_code range="1:" level="fatal" description="Failure" /> - </stdio> - - <inputs> - <param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" /> - <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" /> - </inputs> - - <outputs> - <data format="fasta" name="output" /> - </outputs> - - <tests> - <!-- Just test that the tool runs and produces vaguely correct output --> - <test> - <param name="gff_file" value="augustus_sample.gff" format="gff3"/> - <output name="output" file="augustus_sample.fasta" format="fasta"/> - </test> - </tests> - - + <stdio> + <exit_code range="1:" level="fatal" description="Failure" /> + </stdio> + <command> + augustus_to_proteindb.rb $gff_file -o $output $coords + </command> + <inputs> + <param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" /> + <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" /> + </inputs> + <outputs> + <data format="fasta" name="output" /> + </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="gff_file" value="augustus_sample.gff" format="gff3"/> + <output name="output" file="augustus_sample.fasta" format="fasta"/> + </test> + </tests> <help> **What it does** @@ -42,11 +31,5 @@ Extract proteins from gff3 and encode genomic coordinates in the fasta header. Currently this only works with gff3 generated using the Augustus gene finder ----- - -**References** - - </help> - </tool> |
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| diff -r a85c8de9630a -r 68d8c9e521d7 mzid_to_protxml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mzid_to_protxml.xml Tue Oct 20 20:34:50 2015 -0400 |
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| @@ -0,0 +1,53 @@ +<tool id="mzid_to_protxml" name="mzIdentML to protXML" version="1.0.1"> + <description>Convert mzIdentML to protXML</description> + + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + <requirement type="package" version="2.2.29">blast+</requirement> + </requirements> + + <command> + mzid_to_protxml.rb $mzid_file + + -o $output + </command> + + <stdio> + <exit_code range="1:" level="fatal" description="Failure" /> + </stdio> + + <inputs> + + <param name="mzid_file" type="data" format="mzid" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/> + + </inputs> + + <outputs> + <data format="protxml" name="output" /> + </outputs> + + + <tests> + <test> + <param name="mzid_file" value="PeptideShaker_tiny.mzid" format="mzid"/> + <output name="output" format="protxml"> + <assert_contents> + <has_text text="JEMP01000061" /> + </assert_contents> + </output> + </test> + </tests> + + <help> + +**What it does** + +Roughly converts mzIdentML to protXML. + +At the present time, the conversion is really only designed to work with mzIdentML files produced by PeptideShaker and to produce protXML files suitable for input to protk proteogenomics tools. + + + </help> + +</tool> |
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| diff -r a85c8de9630a -r 68d8c9e521d7 protxml_to_gff.xml --- a/protxml_to_gff.xml Thu Mar 26 20:16:00 2015 -0400 +++ b/protxml_to_gff.xml Tue Oct 20 20:34:50 2015 -0400 |
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| b'@@ -1,102 +1,120 @@\n <tool id="protxml_to_gff" name="Proteomics to GFF" version="1.1.0">\n-\t<description>Export Proteomics Data to GFF</description>\n+ <description>Export Proteomics Data to GFF</description>\n+ <requirements>\n+ <container type="docker">iracooke/protk-1.4.3</container>\n+ <requirement type="package" version="1.4.3">protk</requirement>\n+ <requirement type="package" version="2.2.29">blast+</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Failure" />\n+ </stdio>\n+ <command>\n+ protxml_to_gff.rb $protxml_file \n+ #if $database.source_select=="built_in":\n+ -d $database.dbkey\n+ #else \n+ -d $database.fasta_file\n+ #end if\n+ -c $gene_file\n+ #if str( $gffidpattern ):\n+ --gff-idregex=\'$gffidpattern\'\n+ #end if\n \n-\t<requirements>\n-\t\t<container type="docker">iracooke/protk-1.4.1</container>\t\t\n-\t\t<requirement type="package" version="1.4">protk</requirement>\n-\t\t<requirement type="package" version="2.2.29">blast+</requirement>\n- </requirements>\n+ #if str( $genomeidpattern ):\n+ --genome-idregex=\'$genomeidpattern\'\n+ #end if\n \n-\t<command>\n-\t\tprotxml_to_gff.rb $protxml_file \n-\t\t\n-\t\t#if $database.source_select=="built_in":\n-\t\t-d $database.dbkey\n-\t\t#else \n-\t\t-d $database.fasta_file\n-\t\t#end if\n+ #if str( $ignorepattern ):\n+ --ignore-regex=\'$ignorepattern\'\n+ #end if\n+ \n+ --threshold=$peptide_threshold\n+ --prot-threshold=$prot_threshold\n+ $stack_charges\n+ -o $output\n+ </command>\n+ <inputs>\n+ <conditional name="database">\n+ <param name="source_select" type="select" label="Database source used for Proteomics Searches" help="Database should be an amino acid fasta file with entry id\'s that can be parsed to obtain contig or scaffold ids referenced in your gff file">\n+ <option value="input_ref">Your Upload File</option>\n+ <option value="built_in">Built-In</option>\n+ </param>\n+ <when value="built_in">\n+ <param name="dbkey" type="select" format="text" >\n+ <label>Database</label>\n+ <options from_file="pepxml_databases.loc">\n+ <column name="name" index="0" />\n+ <column name="value" index="2" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="input_ref">\n+ <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />\n+ </when>\n+ </conditional>\n+ <param name="protxml_file" type="data" format="protxml" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/>\n+ <param name="gene_file" type="data" format="gff3" multiple="false" label="Protein coordinates" help="A gff3 file with coordinates for all protein entries used for proteomics searches. Coordinates should correspond to entries in the genome fasta file"/>\n+ <param name="peptide_threshold" label="Peptide Probability Threshold" type="float" value="0.95" min="0" max="1" help="Only peptides within accepted proteins and passing this threshold will appear in the output"/>\n+ <param name="prot_threshold" label="Protein Probability Threshold" type="float" value="0.99" min="0" max="1" help="Only peptides within proteins passing this threshold will appear in the output"/>\n+ <param name="stack_charges" value="false" type="boolean" label="Peptides with different charges get separate gff entries" help="" truevalue="--stack-charge-states" falsevalue="" />\n+ <param name="gffidpattern" size="40" type="text" value="lcl\\|([^ ]*)" label="gff id regex" help="Regex with capture group for parsing gff ids from protein ids'..b'c ids from protein ids">\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ <remove value="'"/>\n+ </valid>\n+ <mapping initial="none">\n+ <add source="'" target="__sq__"/>\n+ </mapping>\n+ </sanitizer>\n+ </param> \n \n-\t\t--gff-idregex=\'$gffidpattern\'\n-\t\t\n-\t\t-o $output\n+ <param name="ignorepattern" size="40" type="text" label="ignore regex" help="Regex to match protein ids that we should ignore completely">\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ <remove value="'"/>\n+ </valid>\n+ <mapping initial="none">\n+ <add source="'" target="__sq__"/>\n+ </mapping>\n+ </sanitizer>\n+ </param> \n \n \n-\t</command>\n \n-\t<stdio>\n-\t\t<exit_code range="1:" level="fatal" description="Failure" />\n-\t</stdio>\n-\n-\t<inputs>\t\n-\t\t<conditional name="database">\n-\t\t\t<param name="source_select" type="select" label="Database source used for Proteomics Searches" help="Database should be an amino acid fasta file with entry id\'s that can be parsed to obtain contig or scaffold ids referenced in your gff file">\n-\t\t\t\t<option value="input_ref">Your Upload File</option>\n-\t\t\t\t<option value="built_in">Built-In</option>\n-\t\t\t</param>\n-\t\t\t<when value="built_in">\n-\t\t\t\t<param name="dbkey" type="select" format="text" >\n-\t\t\t\t\t<label>Database</label>\n-\t\t\t\t\t<options from_file="pepxml_databases.loc">\n-\t\t\t\t\t\t<column name="name" index="0" />\n-\t\t\t\t\t\t<column name="value" index="2" />\n-\t\t\t\t\t</options>\n-\t\t\t\t</param>\n-\t\t\t</when>\n-\t\t\t<when value="input_ref">\n-\t\t\t\t<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />\n-\t\t\t</when>\n-\t\t</conditional>\n-\t\t\n-\t\t<param name="protxml_file" type="data" format="protxml" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/>\n-\n-\t\t<param name="gene_file" type="data" format="gff3" multiple="false" label="Protein coordinates" help="A gff3 file with coordinates for all protein entries used for proteomics searches. Coordinates should correspond to entries in the genome fasta file"/>\n+ </inputs>\n+ <outputs>\n+ <data format="gff3" name="output" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="source_select" value="input_ref"/>\n+ <param name="fasta_file" value="small_prot.fasta" format="fasta"/>\n \n-\t\t<param name="gffidpattern" size="40" type="text" value="lcl\\|([^ ]*)" label="gff id regex" help="Regex with capture group for parsing gff ids from protein ids">\n-\t \t<sanitizer>\n- \t<valid initial="string.printable">\n- \t<remove value="'"/>\n- \t</valid>\n- \t<mapping initial="none">\n- \t<add source="'" target="__sq__"/>\n- \t</mapping>\n- \t\t</sanitizer>\n-\t </param>\n-\n-\t</inputs>\n-\n-\t<outputs>\n-\t\t<data format="gff3" name="output" />\n-\t</outputs>\n-\n-\n-\t<tests>\n-\t <test>\n-\t \t<param name="source_select" value="input_ref"/>\n-\t \t<param name="fasta_file" value="small_prot.fasta" format="fasta"/>\n-\n-\t <param name="protxml_file" value="small.prot.xml" format="protxml"/>\n-\t <param name="gene_file" value="small_combined.gff" format="gff3"/>\n-\t <output name="output" format="gff3">\n-\t <assert_contents>\n-\t <has_text text="polypeptide" />\n-\t </assert_contents>\n-\t </output>\n-\t </test>\n-\t</tests>\n-\n- <help>\n+ <param name="protxml_file" value="small.prot.xml" format="protxml"/>\n+ <param name="gene_file" value="small_combined.gff" format="gff3"/>\n+ <output name="output" format="gff3">\n+ <assert_contents>\n+ <has_text text="polypeptide" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n \n **What it does**\n \n Exports peptides and proteins to gff\n \n-----\n-\n-**References**\n-\n-\n- </help>\n-\n+ </help>\n </tool>\n' |
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| diff -r a85c8de9630a -r 68d8c9e521d7 repository_dependencies.xml --- a/repository_dependencies.xml Thu Mar 26 20:16:00 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Proteomics datatypes"> - <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> - </repositories> |
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| diff -r a85c8de9630a -r 68d8c9e521d7 test-data/PeptideShaker_tiny.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PeptideShaker_tiny.mzid Tue Oct 20 20:34:50 2015 -0400 |
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| b'@@ -0,0 +1,1725 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<MzIdentML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n+xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"\n+id="PeptideShaker v0.38.2"\n+xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd"\n+version="1.1.0" creationDate="2015-05-07T01:24:08">\n+ <cvList>\n+ <cv id="PSI-MS"\n+ uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"\n+ version="3.73.0" fullName="PSI-MS" />\n+ <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo"\n+ fullName="UNIMOD" />\n+ <cv id="UO"\n+ uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"\n+ fullName="UNIT-ONTOLOGY" />\n+ <cv id="PRIDE"\n+ uri="http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo"\n+ fullName="PRIDE" />\n+ </cvList>\n+ <AnalysisSoftwareList>\n+ <AnalysisSoftware name="PeptideShaker" version="0.38.2"\n+ id="ID_software" uri="http://peptide-shaker.googlecode.com">\n+ <ContactRole contact_ref="PS_DEV">\n+ <Role>\n+ <cvParam cvRef="PSI-MS" accession="MS:1001267"\n+ name="software vendor" value="CompOmics" />\n+ </Role>\n+ </ContactRole>\n+ <SoftwareName>\n+ <cvParam cvRef="PSI-MS" accession="MS:1002458"\n+ name="PeptideShaker" />\n+ </SoftwareName>\n+ <Customizations>No customisations</Customizations>\n+ </AnalysisSoftware>\n+ </AnalysisSoftwareList>\n+ <Provider id="PROVIDER">\n+ <ContactRole contact_ref="PROVIDER">\n+ <Role>\n+ <cvParam cvRef="PSI-MS" accession="MS:1001271"\n+ name="researcher" />\n+ </Role>\n+ </ContactRole>\n+ </Provider>\n+ <AuditCollection>\n+ <Person firstName="Proteomics" lastName="Galaxy" id="PROVIDER">\n+ <cvParam cvRef="PSI-MS" accession="MS:1000587"\n+ name="contact address" value="galaxyp@umn.edu" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1000589"\n+ name="contact email" value="galaxyp@umn.edu" />\n+ <Affiliation organization_ref="ORG_DOC_OWNER" />\n+ </Person>\n+ <Organization name="University of Minnesota"\n+ id="ORG_DOC_OWNER">\n+ <cvParam cvRef="PSI-MS" accession="MS:1000586"\n+ name="contact name" value="University of Minnesota" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1000587"\n+ name="contact address"\n+ value="Minneapolis, MN 55455, Vereinigte Staaten" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1000589"\n+ name="contact email" value="galaxyp@umn.edu" />\n+ </Organization>\n+ <Organization name="PeptideShaker developers" id="PS_DEV">\n+ <cvParam cvRef="PSI-MS" accession="MS:1000586"\n+ name="contact name" value="PeptideShaker developers" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1000587"\n+ name="contact address"\n+ value="Proteomics Unit, Building for Basic Biology, University of Bergen, Jonas Liesvei 91, N-5009 Bergen, Norway" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1000588"\n+ name="contact url"\n+ value="http://peptide-shaker.googlecode.com" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1000589"\n+ name="contact email"\n+ value="peptide-shaker@googlegroups.com" />\n+ </Organization>\n+ </AuditCollection>\n+ <SequenceCollection>\n+ <DBSequence id="JEMP01000193.1_rev_g3500.t1"\n+ accession="JEMP01000193.1_rev_g3500.t1"\n+ searchDatabase_ref="SearchDB_1">\n+ <cvParam cvRef="PSI-MS" accession="MS:1001088"\n+ name="protein description" value="280755|283436" />\n+ </DBSequence>\n+ <DBSequence id="JEMP01000061.1_rev_g10170.t1"\n+ accession="JEMP01000061.1_rev_g10170.t1"\n+ searchDatabase_ref="SearchDB_1">\n+ <cvParam cvRef="PSI-MS" accession="MS:1001088"\n+ name="protein description" value="36066|38753" />\n+ </DBSequence>\n+ <Peptide id="KSPVYKVHFTR">\n+ <PeptideSequence>KSPVYKVHFTR</PeptideSequence>\n+ </Peptide>\n+ <Peptide id="SKIPFIVIF'..b'tideHypothesis peptideEvidence_ref="PepEv_532">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_531_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_663">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_662_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_963">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_960_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_1108">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1102_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_1474">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1467_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_1796">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1788_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_1829">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1821_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_1958">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1949_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_2003">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1993_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_2093">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_2082_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_2130">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_2101_1" />\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_2118_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_2202">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_2190_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_2204">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_2192_1" />\n+ </PeptideHypothesis>\n+ <PeptideHypothesis peptideEvidence_ref="PepEv_2444">\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_2410_1" />\n+ <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_2430_1" />\n+ </PeptideHypothesis>\n+ <cvParam cvRef="PSI-MS" accession="MS:1002403"\n+ name="group representative" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1002401"\n+ name="leading protein" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1001093"\n+ name="sequence coverage" value="0.28" />\n+ </ProteinDetectionHypothesis>\n+ <cvParam cvRef="PSI-MS" accession="MS:1002470"\n+ name="PeptideShaker protein group score" value="100.0" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1002471"\n+ name="PeptideShaker protein group confidence"\n+ value="100.0" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1002545"\n+ name="PeptideShaker protein confidence type"\n+ value="Confident" />\n+ <cvParam cvRef="PSI-MS" accession="MS:1002415"\n+ name="protein group passes threshold" value="true" />\n+ </ProteinAmbiguityGroup>\n+ <cvParam cvRef="PSI-MS" accession="MS:1002404"\n+ name="count of identified proteins" value="612" />\n+ </ProteinDetectionList>\n+ </AnalysisData>\n+ </DataCollection>\n+</MzIdentML>\n' |
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| diff -r a85c8de9630a -r 68d8c9e521d7 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 26 20:16:00 2015 -0400 +++ b/tool_dependencies.xml Tue Oct 20 20:34:50 2015 -0400 |
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| @@ -1,8 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - + <package name="protk" version="1.4.3"> + <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> <package name="blast+" version="2.2.29"> - <repository changeset_revision="a2ec897aac2c" name="package_blast_plus_2_2_29" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0b75bc235e70" name="package_blast_plus_2_2_29" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - </tool_dependency> |