Mercurial > repos > iracooke > protk_proteogenomics
changeset 2:68d8c9e521d7 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 20:34:50 -0400 |
| parents | a85c8de9630a |
| children | 86fd1757f102 |
| files | gff3_to_fasta.xml mzid_to_protxml.xml protxml_to_gff.xml repository_dependencies.xml test-data/PeptideShaker_tiny.mzid tool_dependencies.xml |
| diffstat | 6 files changed, 1912 insertions(+), 136 deletions(-) [+] |
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--- 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 @@ -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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mzid_to_protxml.xml Tue Oct 20 20:34:50 2015 -0400 @@ -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>
--- 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 @@ -1,102 +1,120 @@ <tool id="protxml_to_gff" name="Proteomics to GFF" version="1.1.0"> - <description>Export Proteomics Data to GFF</description> + <description>Export Proteomics Data to GFF</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> + <stdio> + <exit_code range="1:" level="fatal" description="Failure" /> + </stdio> + <command> + protxml_to_gff.rb $protxml_file + #if $database.source_select=="built_in": + -d $database.dbkey + #else + -d $database.fasta_file + #end if + -c $gene_file + #if str( $gffidpattern ): + --gff-idregex='$gffidpattern' + #end if - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - <requirement type="package" version="2.2.29">blast+</requirement> - </requirements> + #if str( $genomeidpattern ): + --genome-idregex='$genomeidpattern' + #end if - <command> - protxml_to_gff.rb $protxml_file - - #if $database.source_select=="built_in": - -d $database.dbkey - #else - -d $database.fasta_file - #end if + #if str( $ignorepattern ): + --ignore-regex='$ignorepattern' + #end if + + --threshold=$peptide_threshold + --prot-threshold=$prot_threshold + $stack_charges + -o $output + </command> + <inputs> + <conditional name="database"> + <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"> + <option value="input_ref">Your Upload File</option> + <option value="built_in">Built-In</option> + </param> + <when value="built_in"> + <param name="dbkey" type="select" format="text" > + <label>Database</label> + <options from_file="pepxml_databases.loc"> + <column name="name" index="0" /> + <column name="value" index="2" /> + </options> + </param> + </when> + <when value="input_ref"> + <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> + </when> + </conditional> + <param name="protxml_file" type="data" format="protxml" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/> + <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"/> + <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"/> + <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"/> + <param name="stack_charges" value="false" type="boolean" label="Peptides with different charges get separate gff entries" help="" truevalue="--stack-charge-states" falsevalue="" /> + <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"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> - -c $gene_file + <param name="genomeidpattern" size="40" type="text" label="genome id regex" help="Regex with capture group for parsing genomic ids from protein ids"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> - --gff-idregex='$gffidpattern' - - -o $output + <param name="ignorepattern" size="40" type="text" label="ignore regex" help="Regex to match protein ids that we should ignore completely"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> - </command> - <stdio> - <exit_code range="1:" level="fatal" description="Failure" /> - </stdio> - - <inputs> - <conditional name="database"> - <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"> - <option value="input_ref">Your Upload File</option> - <option value="built_in">Built-In</option> - </param> - <when value="built_in"> - <param name="dbkey" type="select" format="text" > - <label>Database</label> - <options from_file="pepxml_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - </when> - <when value="input_ref"> - <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> - </when> - </conditional> - - <param name="protxml_file" type="data" format="protxml" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/> - - <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"/> + </inputs> + <outputs> + <data format="gff3" name="output" /> + </outputs> + <tests> + <test> + <param name="source_select" value="input_ref"/> + <param name="fasta_file" value="small_prot.fasta" format="fasta"/> - <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"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - - </inputs> - - <outputs> - <data format="gff3" name="output" /> - </outputs> - - - <tests> - <test> - <param name="source_select" value="input_ref"/> - <param name="fasta_file" value="small_prot.fasta" format="fasta"/> - - <param name="protxml_file" value="small.prot.xml" format="protxml"/> - <param name="gene_file" value="small_combined.gff" format="gff3"/> - <output name="output" format="gff3"> - <assert_contents> - <has_text text="polypeptide" /> - </assert_contents> - </output> - </test> - </tests> - - <help> + <param name="protxml_file" value="small.prot.xml" format="protxml"/> + <param name="gene_file" value="small_combined.gff" format="gff3"/> + <output name="output" format="gff3"> + <assert_contents> + <has_text text="polypeptide" /> + </assert_contents> + </output> + </test> + </tests> + <help> **What it does** Exports peptides and proteins to gff ----- - -**References** - - - </help> - + </help> </tool>
--- a/repository_dependencies.xml Thu Mar 26 20:16:00 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PeptideShaker_tiny.mzid Tue Oct 20 20:34:50 2015 -0400 @@ -0,0 +1,1725 @@ +<?xml version="1.0" encoding="utf-8"?> +<MzIdentML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" +xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" +id="PeptideShaker v0.38.2" +xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" +version="1.1.0" creationDate="2015-05-07T01:24:08"> + <cvList> + <cv id="PSI-MS" + uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" + version="3.73.0" fullName="PSI-MS" /> + <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" + fullName="UNIMOD" /> + <cv id="UO" + uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" + fullName="UNIT-ONTOLOGY" /> + <cv id="PRIDE" + uri="http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo" + fullName="PRIDE" /> + </cvList> + <AnalysisSoftwareList> + <AnalysisSoftware name="PeptideShaker" version="0.38.2" + id="ID_software" uri="http://peptide-shaker.googlecode.com"> + <ContactRole contact_ref="PS_DEV"> + <Role> + <cvParam cvRef="PSI-MS" accession="MS:1001267" + name="software vendor" value="CompOmics" /> + </Role> + </ContactRole> + <SoftwareName> + <cvParam cvRef="PSI-MS" accession="MS:1002458" + name="PeptideShaker" /> + </SoftwareName> + <Customizations>No customisations</Customizations> + </AnalysisSoftware> + </AnalysisSoftwareList> + <Provider id="PROVIDER"> + <ContactRole contact_ref="PROVIDER"> + <Role> + <cvParam cvRef="PSI-MS" accession="MS:1001271" + name="researcher" /> + </Role> + </ContactRole> + </Provider> + <AuditCollection> + <Person firstName="Proteomics" lastName="Galaxy" id="PROVIDER"> + <cvParam cvRef="PSI-MS" accession="MS:1000587" + name="contact address" value="galaxyp@umn.edu" /> + <cvParam cvRef="PSI-MS" accession="MS:1000589" + name="contact 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+ <cvParam cvRef="PSI-MS" accession="MS:1000589" + name="contact email" + value="peptide-shaker@googlegroups.com" /> + </Organization> + </AuditCollection> + <SequenceCollection> + <DBSequence id="JEMP01000193.1_rev_g3500.t1" + accession="JEMP01000193.1_rev_g3500.t1" + searchDatabase_ref="SearchDB_1"> + <cvParam cvRef="PSI-MS" accession="MS:1001088" + name="protein description" value="280755|283436" /> + </DBSequence> + <DBSequence id="JEMP01000061.1_rev_g10170.t1" + accession="JEMP01000061.1_rev_g10170.t1" + searchDatabase_ref="SearchDB_1"> + <cvParam cvRef="PSI-MS" accession="MS:1001088" + name="protein description" value="36066|38753" /> + </DBSequence> + <Peptide id="KSPVYKVHFTR"> + <PeptideSequence>KSPVYKVHFTR</PeptideSequence> + </Peptide> + <Peptide id="SKIPFIVIFDPIEAAR"> + <PeptideSequence>SQIPFLVLFDPIEAAR</PeptideSequence> + </Peptide> + <Peptide id="SSGNWINIFNPATPSFR"> + <PeptideSequence>SSGNWLNLFNPATPSFR</PeptideSequence> + </Peptide> + <Peptide id="GGIDSWNAIGYIPVKDFDYK"> + 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--- a/tool_dependencies.xml Thu Mar 26 20:16:00 2015 -0400 +++ b/tool_dependencies.xml Tue Oct 20 20:34:50 2015 -0400 @@ -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>