Mercurial > repos > iracooke > omssa
changeset 8:4294476e3f83 draft default tip
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 20:30:52 -0400 |
| parents | 51f6c6446e69 |
| children | |
| files | omssa.xml repository_dependencies.xml tool_dependencies.xml |
| diffstat | 3 files changed, 163 insertions(+), 185 deletions(-) [+] |
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--- a/omssa.xml Thu Mar 26 20:04:12 2015 -0400 +++ b/omssa.xml Tue Oct 20 20:30:52 2015 -0400 @@ -1,184 +1,162 @@ -<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.1.0"> - - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - <requirement type="package" version="2.1.9">omssa</requirement> - <requirement type="package" version="2.2.29">blast+</requirement> - </requirements> - - - <description>Run an OMSSA MS/MS Search</description> - - <command>omssa_search.rb +<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.1.1"> + <description>Run an OMSSA MS/MS Search</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + <requirement type="package" version="2.1.9">omssa</requirement> + <requirement type="package" version="2.2.29">blast+</requirement> + </requirements> + <command>omssa_search.rb - #if $database.source_select=="built_in": - -d $database.dbkey - #else - -d $database.fasta_file - #end if - - --var-mods=' - $variable_mods - ' - - --fix-mods=' - $fixed_mods - ' - - --searched-ions=' - $searched_ions - ' - - $input_file - -o $output - -r - - --enzyme=$enzyme - - --precursor-ion-tol-units=$precursor_tolu - - -v $missed_cleavages - - -f $fragment_ion_tol + #if $database.source_select=="built_in": + -d $database.dbkey + #else + -d $database.fasta_file + #end if + --var-mods=' + $variable_mods + ' - -p $precursor_ion_tol - - --num-peaks-for-multi-isotope-search $multi_isotope - - $use_average_mass - $respect_precursor_charges + --fix-mods=' + $fixed_mods + ' - --max-hit-expect $max_hit_expect + --searched-ions=' + $searched_ions + ' - --intensity-cut-off $intensity_cut_off - - </command> - + $input_file + -o $output + -r - <inputs> - <conditional name="database"> - <param name="source_select" type="select" label="Database source"> - <option value="built_in">Built-In</option> - <option selected="true" value="input_ref">Uploaded fasta file</option> - </param> - <when value="built_in"> - <param name="dbkey" type="select" format="text" > - <label>Database</label> - <options from_file="pepxml_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - </when> - <when value="input_ref"> - <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> - </when> - </conditional> - - <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/> + --enzyme=$enzyme + --precursor-ion-tol-units=$precursor_tolu + -v $missed_cleavages + -f $fragment_ion_tol + -p $precursor_ion_tol + --num-peaks-for-multi-isotope-search $multi_isotope - <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while - clicking to select multiple items"> - <options from_file="omssa_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> + $use_average_mass + $respect_precursor_charges + + --max-hit-expect $max_hit_expect + --intensity-cut-off $intensity_cut_off - <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while - clicking to select multiple items"> - <options from_file="omssa_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - - - <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> - <label>Missed Cleavages Allowed</label> - <option value="0">0</option> - <option value="1">1</option> - <option selected="true" value="2">2</option> - </param> - - <param name="enzyme" type="select" format="text"> - <label>Enzyme</label> - <option value="0">Trypsin</option> - <option value="1">Arg-C</option> - <option value="2">CNBr</option> - <option value="3">Chymotrypsin (FYWL)</option> - <option value="4">Formic Acid</option> - <option value="5">Lys-C</option> - <option value="6">Lys-C, no P rule</option> - <option value="7">Pepsin A</option> - <option value="8">Trypsin+CNBr</option> - <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option> - <option value="10">Trypsin, no P rule</option> - <option value="11">Whole protein</option> - <option value="12">Asp-N</option> - <option value="13">Glu-C</option> - <option value="14">Asp-N+Glu-C</option> - <option value="15">Top-Down</option> - <option value="16">Semi-Tryptic</option> - <option value="17">No Enzyme</option> - <option value="18">Chymotrypsin, no P rule (FYWL)</option> - <option value="19">Asp-N (DE)</option> - <option value="20">Glu-C (DE)</option> - <option value="21">Lys-N (K)</option> - <option value="22">Thermolysin, no P rule</option> - <option value="23">Semi-Chymotrypsin (FYWL)</option> - <option value="24">Semi-Glu-C</option> - </param> + </command> + <inputs> + <conditional name="database"> + <param name="source_select" type="select" label="Database source"> + <option value="built_in">Built-In</option> + <option selected="true" value="input_ref">Uploaded fasta file</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="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/> + <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while + clicking to select multiple items"> + <options from_file="omssa_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="2" /> + </options> + </param> + <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" + help="Hold the appropriate key while clicking to select multiple items"> + <options from_file="omssa_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="2" /> + </options> + </param> + <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> + <label>Missed Cleavages Allowed</label> + <option value="0">0</option> + <option value="1">1</option> + <option selected="true" value="2">2</option> + </param> + <param name="enzyme" type="select" format="text"> + <label>Enzyme</label> + <option value="0">Trypsin</option> + <option value="1">Arg-C</option> + <option value="2">CNBr</option> + <option value="3">Chymotrypsin (FYWL)</option> + <option value="4">Formic Acid</option> + <option value="5">Lys-C</option> + <option value="6">Lys-C, no P rule</option> + <option value="7">Pepsin A</option> + <option value="8">Trypsin+CNBr</option> + <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option> + <option value="10">Trypsin, no P rule</option> + <option value="11">Whole protein</option> + <option value="12">Asp-N</option> + <option value="13">Glu-C</option> + <option value="14">Asp-N+Glu-C</option> + <option value="15">Top-Down</option> + <option value="16">Semi-Tryptic</option> + <option value="17">No Enzyme</option> + <option value="18">Chymotrypsin, no P rule (FYWL)</option> + <option value="19">Asp-N (DE)</option> + <option value="20">Glu-C (DE)</option> + <option value="21">Lys-N (K)</option> + <option value="22">Thermolysin, no P rule</option> + <option value="23">Semi-Chymotrypsin (FYWL)</option> + <option value="24">Semi-Glu-C</option> + </param> - <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/> - <param name="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="10000.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he--> - <param name="intensity_cut_off" help="Peak intensity cut-off as a fraction of maximum peak intensity" type="float" value="0.0005" min="0" max="1" label="Peak intensity cut-off"/><!-- -ci--> + <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/> + <param name="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="10000.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he--> + <param name="intensity_cut_off" help="Peak intensity cut-off as a fraction of maximum peak intensity" type="float" value="0.0005" min="0" max="1" label="Peak intensity cut-off"/><!-- -ci--> + <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/> + <param name="precursor_tolu" type="select" format="text"> + <label>Precursor Ion Tolerance Units</label> + <option value="ppm">ppm</option> + <option value="Da">Da</option> + </param> - <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/> - <param name="precursor_tolu" type="select" format="text"> - <label>Precursor Ion Tolerance Units</label> - <option value="ppm">ppm</option> - <option value="Da">Da</option> - </param> - - <param name="use_average_mass" type="boolean" label="Use average precursor masses" help="Match precursor to average mass of the parent ion instead of its monoisotopic mass" truevalue="-a average" falsevalue=""/> - <param name="respect_precursor_charges" type="boolean" label="Respect precursor charges" help="Use precursor charge information in input file rather than OMSSA's inferred value" truevalue="--respect-charges" falsevalue=""/> - - <param name="multi_isotope" type="select" format="text" help="Include this many neighbouring peaks when searching for a match to the precursor mass. Only used when doing monoisotopic search"> - <label>Multi-isotope search.</label> - <option value="0">0</option> - <option value="1">1</option> - <option value="2">2</option> - <option value="3">3</option> - <option value="4">4</option> - </param> + <param name="use_average_mass" type="boolean" label="Use average precursor masses" help="Match precursor to average mass of the parent ion instead of its monoisotopic mass" truevalue="-a average" falsevalue=""/> + <param name="respect_precursor_charges" type="boolean" label="Respect precursor charges" help="Use precursor charge information in input file rather than OMSSA's inferred value" truevalue="--respect-charges" falsevalue=""/> + + <param name="multi_isotope" type="select" format="text" help="Include this many neighbouring peaks when searching for a match to the precursor mass. Only used when doing monoisotopic search"> + <label>Multi-isotope search.</label> + <option value="0">0</option> + <option value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + <option value="4">4</option> + </param> - <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help=""> - <option value="0">a</option> - <option selected="true" value="1">b</option> - <option value="2">c</option> - <option value="3">x</option> - <option selected="true" value="4">y</option> - <option value="5">zdot</option> - <option value="10">adot</option> - <option value="11">x-CO2</option> - <option value="12">adot-CO2</option> - </param> - - </inputs> + <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help=""> + <option value="0">a</option> + <option selected="true" value="1">b</option> + <option value="2">c</option> + <option value="3">x</option> + <option selected="true" value="4">y</option> + <option value="5">zdot</option> + <option value="10">adot</option> + <option value="11">x-CO2</option> + <option value="12">adot-CO2</option> + </param> - <outputs> - <data format="raw_pepxml" name="output" metadata_source="input_file" label="omssa_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.pepXML"/> - </outputs> - - <tests> - <!-- Just test that the tool runs and produces vaguely correct output --> - <test> - <param name="source_select" value="input_ref"/> - <param name="fasta_file" value="AASequences.fasta" format="fasta"/> - <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d.mgf" format="mgf"/> + </inputs> + <outputs> + <data format="raw_pepxml" name="output" metadata_source="input_file" label="omssa_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.pepXML"/> + </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="source_select" value="input_ref"/> + <param name="fasta_file" value="AASequences.fasta" format="fasta"/> + <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d.mgf" format="mgf"/> <param name="max_hit_expect" value="1000"/> <param name="precursor_ion_tol" value="1.2"/> <param name="precursor_tolu" value="Da"/> @@ -186,15 +164,15 @@ <param name="variable_mods" value="1"/> - <output name="output" format="raw_pepxml"> - <assert_contents> - <has_text text="VLFSQAQVYELERRFK" /> - </assert_contents> - </output> - </test> - </tests> + <output name="output" format="raw_pepxml"> + <assert_contents> + <has_text text="VLFSQAQVYELERRFK" /> + </assert_contents> + </output> + </test> + </tests> - <help> + <help> **What it does** Runs an MS/MS database search using the OMSSA search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. @@ -207,5 +185,5 @@ Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004). - </help> + </help> </tool>
--- a/repository_dependencies.xml Thu Mar 26 20:04:12 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>
--- a/tool_dependencies.xml Thu Mar 26 20:04:12 2015 -0400 +++ b/tool_dependencies.xml Tue Oct 20 20:30:52 2015 -0400 @@ -1,8 +1,12 @@ <?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> - + <package name="omssa" version="2.1.9"> + <repository changeset_revision="986d3f456c59" name="package_omssa_2_1_9" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> </tool_dependency>