| Previous changeset 7:51f6c6446e69 (2015-03-26) |
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Commit message:
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty |
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modified:
omssa.xml tool_dependencies.xml |
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removed:
repository_dependencies.xml |
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| diff -r 51f6c6446e69 -r 4294476e3f83 omssa.xml --- a/omssa.xml Thu Mar 26 20:04:12 2015 -0400 +++ b/omssa.xml Tue Oct 20 20:30:52 2015 -0400 |
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| b'@@ -1,184 +1,162 @@\n-<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.1.0">\n-\n- <requirements>\n- <container type="docker">iracooke/protk-1.4.1</container>\n-\t <requirement type="package" version="1.4">protk</requirement>\n- \t<requirement type="package" version="2.1.9">omssa</requirement>\n- \t<requirement type="package" version="2.2.29">blast+</requirement>\n- </requirements>\n-\n-\n-\t<description>Run an OMSSA MS/MS Search</description>\n-\t\t\n-\t<command>omssa_search.rb\n+<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.1.1">\n+ <description>Run an OMSSA MS/MS Search</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="2.1.9">omssa</requirement>\n+ <requirement type="package" version="2.2.29">blast+</requirement>\n+ </requirements>\n+ <command>omssa_search.rb\n \n-\t\t#if $database.source_select=="built_in":\n-\t\t-d $database.dbkey \n-\t\t#else\n-\t\t-d $database.fasta_file\n-\t\t#end if\n-\t\t\n-\t\t--var-mods=\'\n-\t\t$variable_mods\n-\t\t\'\n-\t\t\n-\t\t--fix-mods=\'\n-\t\t$fixed_mods\n-\t\t\'\n-\t\t\n-\t\t--searched-ions=\'\n-\t\t$searched_ions\n-\t\t\'\n-\t\t\n-\t\t$input_file \n-\t\t-o $output \n-\t\t-r \n-\n-\t\t--enzyme=$enzyme \n-\n-\t\t--precursor-ion-tol-units=$precursor_tolu \n-\n-\t\t-v $missed_cleavages \n-\n-\t\t-f $fragment_ion_tol \n+ #if $database.source_select=="built_in":\n+ -d $database.dbkey \n+ #else\n+ -d $database.fasta_file\n+ #end if\n+ --var-mods=\'\n+ $variable_mods\n+ \'\n \n-\t\t-p $precursor_ion_tol \n-\n-\t\t--num-peaks-for-multi-isotope-search $multi_isotope \n-\n-\t\t$use_average_mass \n-\t\t$respect_precursor_charges \n+ --fix-mods=\'\n+ $fixed_mods\n+ \'\n \n-\t\t--max-hit-expect $max_hit_expect \n+ --searched-ions=\'\n+ $searched_ions\n+ \'\n \n-\t\t--intensity-cut-off $intensity_cut_off\n-\n-\t</command>\n-\t\n+ $input_file \n+ -o $output \n+ -r \n \n-\t<inputs>\t\n-\t\t<conditional name="database">\n-\t\t\t<param name="source_select" type="select" label="Database source">\n-\t\t\t\t<option value="built_in">Built-In</option>\n-\t\t\t\t<option selected="true" value="input_ref">Uploaded fasta file</option>\n-\t\t\t</param>\n-\t\t\t<when value="built_in">\n-\t\t\t\t<param name="dbkey" type="select" format="text" >\n-\t\t\t\t\t<label>Database</label>\n-\t\t\t\t\t<options from_file="pepxml_databases.loc">\n-\t\t\t\t\t\t<column name="name" index="0" />\n-\t\t\t\t\t\t<column name="value" index="2" />\n-\t\t\t\t\t</options>\n-\t\t\t\t</param>\n-\t\t\t</when>\n-\t\t\t<when value="input_ref">\n-\t\t\t\t<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />\n-\t\t\t</when>\n-\t\t</conditional>\n-\t\t\n-\t\t<param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/>\t\t\n+ --enzyme=$enzyme \n+ --precursor-ion-tol-units=$precursor_tolu \n+ -v $missed_cleavages \n+ -f $fragment_ion_tol \n+ -p $precursor_ion_tol \n+ --num-peaks-for-multi-isotope-search $multi_isotope \n \n-\t\t<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while\n-\t\t\tclicking to select multiple items">\n-\t\t\t<options from_file="omssa_mods.loc">\n-\t\t\t\t<column name="name" index="0" />\n-\t\t\t\t<column name="value" index="2" />\n-\t\t\t</options>\n-\t\t</param>\t\t\n+ $use_average_mass \n+ $respect_precursor_charges \n+\n+ --max-hit-expect $max_hit_expect \n+ --intensity-cut-off $intensity_cut_off\n \n-\t\t<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while\n-\t\tclicking to select multiple items">\n-\t\t\t<options from_file="omssa_mods.loc">\n-\t\t\t\t<column name="name" index="0" />\n-\t\t\t\t<column name="value" index="2" />\n-\t\t\t</options>\n-\t\t</param>\n-\n-\t\t\n-\t\t<param name="missed_cleavages" type="select" format="text" help="Allow peptides t'..b'="boolean" label="Respect precursor charges" help="Use precursor charge information in input file rather than OMSSA\'s inferred value" truevalue="--respect-charges" falsevalue=""/>\n+\n+ <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">\n+ <label>Multi-isotope search.</label>\n+ <option value="0">0</option>\n+ <option value="1">1</option>\n+ <option value="2">2</option>\n+ <option value="3">3</option>\n+ <option value="4">4</option>\n+ </param>\n \n-\t\t<param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help="">\n-\t\t <option value="0">a</option>\n-\t\t\t<option selected="true" value="1">b</option>\n-\t\t\t<option value="2">c</option>\n-\t\t\t<option value="3">x</option>\n-\t\t\t<option selected="true" value="4">y</option>\n-\t\t\t<option value="5">zdot</option>\n-\t\t\t<option value="10">adot</option>\n-\t\t\t<option value="11">x-CO2</option>\n-\t\t\t<option value="12">adot-CO2</option>\n-\t\t</param>\n-\t\t\n-\t</inputs>\n+ <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help="">\n+ <option value="0">a</option>\n+ <option selected="true" value="1">b</option>\n+ <option value="2">c</option>\n+ <option value="3">x</option>\n+ <option selected="true" value="4">y</option>\n+ <option value="5">zdot</option>\n+ <option value="10">adot</option>\n+ <option value="11">x-CO2</option>\n+ <option value="12">adot-CO2</option>\n+ </param>\n \n-\t<outputs>\n-\t\t<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"/>\n-\t</outputs>\n-\n-\t<tests>\n-\t\t<!-- Just test that the tool runs and produces vaguely correct output -->\n-\t\t<test>\n-\t\t <param name="source_select" value="input_ref"/>\n-\t\t <param name="fasta_file" value="AASequences.fasta" format="fasta"/>\n-\t\t <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d.mgf" format="mgf"/>\n+ </inputs>\n+ <outputs>\n+ <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"/>\n+ </outputs>\n+ <tests>\n+ <!-- Just test that the tool runs and produces vaguely correct output -->\n+ <test>\n+ <param name="source_select" value="input_ref"/>\n+ <param name="fasta_file" value="AASequences.fasta" format="fasta"/>\n+ <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d.mgf" format="mgf"/>\n <param name="max_hit_expect" value="1000"/>\n <param name="precursor_ion_tol" value="1.2"/>\n <param name="precursor_tolu" value="Da"/>\n@@ -186,15 +164,15 @@\n <param name="variable_mods" value="1"/>\n \n \n-\t\t <output name="output" format="raw_pepxml">\n-\t\t <assert_contents>\n-\t\t\t\t\t<has_text text="VLFSQAQVYELERRFK" />\n-\t\t </assert_contents>\n-\t\t </output>\n-\t\t</test>\n-\t</tests>\n+ <output name="output" format="raw_pepxml">\n+ <assert_contents>\n+ <has_text text="VLFSQAQVYELERRFK" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n \n-\t<help>\n+ <help>\n **What it does**\n \n 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.\n@@ -207,5 +185,5 @@\n \n Geer L. Y., et al. \xe2\x80\x9cOpen mass spectrometry search algorithm\xe2\x80\x9d *J. Proteome Res.* 3(5), 958-964 (2004).\n \n-\t</help>\n+ </help>\n </tool>\n' |
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| diff -r 51f6c6446e69 -r 4294476e3f83 repository_dependencies.xml --- a/repository_dependencies.xml Thu Mar 26 20:04:12 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 51f6c6446e69 -r 4294476e3f83 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 26 20:04:12 2015 -0400 +++ b/tool_dependencies.xml Tue Oct 20 20:30:52 2015 -0400 |
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| @@ -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> |