| Previous changeset 14:9d6e0ad4d600 (2015-03-26) Next changeset 16:63b15b77e56c (2015-10-21) |
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Commit message:
planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty |
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modified:
tandem.xml tandem_to_pepxml.xml |
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added:
tool_dependencies.xml |
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removed:
repository_dependencies.xml |
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| diff -r 9d6e0ad4d600 -r 0faaab4f192a repository_dependencies.xml --- a/repository_dependencies.xml Thu Mar 26 19:53:53 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 9d6e0ad4d600 -r 0faaab4f192a tandem.xml --- a/tandem.xml Thu Mar 26 19:53:53 2015 -0400 +++ b/tandem.xml Tue Oct 20 20:47:05 2015 -0400 |
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| b'@@ -1,206 +1,180 @@\n-<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.0">\n-\n+<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.1">\n+ <description>Run an X!Tandem Search</description>\n <requirements>\n- <container type="docker">iracooke/protk-1.4.1</container>\n-\t <requirement type="package" version="1.4">protk</requirement>\n- </requirements>\n-\n-\t<description>Run an X!Tandem Search</description>\n+ <container type="docker">iracooke/protk-1.4.3</container>\n+ <requirement type="package" version="1.4.3">protk</requirement>\n+ </requirements>\n+ <command>\n+ #if $database.source_select=="built_in":\n+ tandem_search.rb -d $database.dbkey \n+ #else\n+ tandem_search.rb -d $database.fasta_file\n+ #end if\n \n-\t<command>\n-\t\t#if $database.source_select=="built_in":\n-\t\ttandem_search.rb -d $database.dbkey \n-\t\t#else \n-\t\ttandem_search.rb -d $database.fasta_file\n-\t\t#end if\n-\n-\t\t#if $tandem_params.source_select=="built_in":\n-\t\t-T $tandem_params.paramskey \n-\t\t#else \n-\t\t-T $tandem_params.params_file\n-\t\t#end if\n+ #if $tandem_params.source_select=="built_in":\n+ -T $tandem_params.paramskey \n+ #else \n+ -T $tandem_params.params_file\n+ #end if\n \n \n-\t\t--var-mods=\'\n-\t\t$variable_mods\n-\t\t#for $custom_variable_mod in $custom_variable_mods:\n-\t\t,${custom_variable_mod.custom_mod}\n-\t\t#end for\n-\t\t\'\n+ --var-mods=\'\n+ $variable_mods\n+ #for $custom_variable_mod in $custom_variable_mods:\n+ ,${custom_variable_mod.custom_mod}\n+ #end for\n+ \'\n \n-\t\t--fix-mods=\'\n-\t\t$fixed_mods\n-\t\t#for $custom_fix_mod in $custom_fix_mods:\n-\t\t,${custom_fix_mod.custom_mod}\n-\t\t#end for\n-\t\t\'\n-\n-\t\t$input_file -o $output -r \n-\n-\t\t--enzyme=$enzyme \n+ --fix-mods=\'\n+ $fixed_mods\n+ #for $custom_fix_mod in $custom_fix_mods:\n+ ,${custom_fix_mod.custom_mod}\n+ #end for\n+ \'\n \n-\t\t--precursor-ion-tol-units=$precursor_tolu \n-\n-\t\t-v $missed_cleavages \n+ $input_file -o $output -r \n \n-\t\t-f $fragment_ion_tol \n-\n-\t\t-p $precursor_ion_tol\n-\n-\t\t$allow_multi_isotope_search \n+ --enzyme=$enzyme \n \n-\t\t$acetyl_protein_nterm\n-\n-\t\t$cleavage_semi\n-\n-\t\t$keep_spectra\n-\n-\t\t--threads $threads\n-\t\t\n-\t</command>\n+ --precursor-ion-tol-units=$precursor_tolu \n+ -v $missed_cleavages \n+ -f $fragment_ion_tol \n+ -p $precursor_ion_tol\n+ $allow_multi_isotope_search \n+ $acetyl_protein_nterm\n+ $cleavage_semi\n+ $keep_spectra\n+ --threads "\\${GALAXY_SLOTS:-12}"\n \n-\t<inputs>\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 value="input_ref" selected="true">Your Upload 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<conditional name="tandem_params">\n-\t\t\t<param name="source_select" type="select" label="Baseline Parameters">\n-\t\t\t\t<option value="built_in" selected="true">Built-In</option>\n-\t\t\t\t<option value="input_ref">Custom parameter file</option>\n-\t\t\t</param>\n-\t\t\t<when value="built_in">\n-\t\t\t\t<param name="paramskey" type="select" format="text" >\n-\t\t\t\t\t<label>Paramset</label>\n-\t\t\t\t\t<option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>\n-\t\t\t\t <option value="isb_native">ISB Native</option>\t\t\n-\t\t\t\t <option value="gpm">GPM</option>\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="params_file" type="data" format="xml" label="Custom X!Tandem Param'..b'D]</option>\n+ <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option>\n+ <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>\n+ <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>\n+ <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>\n+ </param>\n \n-\t\t\n-\t\t<param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>\n-\n-\t\t<param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>\n-\t\t<param name="precursor_tolu" type="select" format="text">\n-\t\t <label>Precursor Ion Tolerance Units</label>\n-\t\t <option value="ppm">ppm</option>\t\t\n-\t\t\t<option value="Da">Da</option>\n-\t\t</param>\n-\t\t\n-\t\t<param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/>\n-\n-\t</inputs>\n-\n-\n-\t<outputs>\n-\t\t<data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key(\'dbkey\') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>\n-\t</outputs>\n-\n-\t<tests>\n-\t\t<!-- Just test that the tool runs and produces vaguely correct output -->\n-\t\t<test>\n-\t\t <param name="source_select" value="input_ref"/>\n-\t\t <param name="fasta_file" value="testdb.fasta" format="fasta"/>\n-\t\t <param name="input_file" value="tiny.mzML" format="mzml"/>\n-\t\t <output name="output" format="tandem">\n-\t\t <assert_contents>\n-\t\t\t\t\t<has_text text="tandem-style" />\n-\t\t </assert_contents>\n-\t\t </output>\n-\t\t</test>\n-\t</tests>\n+ <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>\n+ <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>\n+ <param name="precursor_tolu" type="select" format="text">\n+ <label>Precursor Ion Tolerance Units</label>\n+ <option value="ppm">ppm</option>\n+ <option value="Da">Da</option>\n+ </param>\n+ <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/>\n+ </inputs>\n+ <outputs>\n+ <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key(\'dbkey\') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>\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="testdb.fasta" format="fasta"/>\n+ <param name="input_file" value="tiny.mzML" format="mzml"/>\n+ <output name="output" format="tandem">\n+ <assert_contents>\n+ <has_text text="tandem-style" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n <help>\n \n **What it does**\n' |
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| diff -r 9d6e0ad4d600 -r 0faaab4f192a tandem_to_pepxml.xml --- a/tandem_to_pepxml.xml Thu Mar 26 19:53:53 2015 -0400 +++ b/tandem_to_pepxml.xml Tue Oct 20 20:47:05 2015 -0400 |
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| @@ -1,38 +1,33 @@ -<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" 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="4.8.0">trans_proteomic_pipeline</requirement> +<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.1"> + <description>Converts a tandem result file to pepXML</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> </requirements> + <command> + tandem_to_pepxml.rb $input_file -o $output + </command> - <description>Converts a tandem result file to pepXML</description> - - <command> - tandem_to_pepxml.rb $input_file -o $output - </command> - - <inputs> - <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/> - </inputs> + <inputs> + <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/> + </inputs> - <outputs> - <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> - </outputs> - - <help> - Convert X!Tandem results to pepXML - </help> - - <tests> - <!-- Just test that the tool runs and produces vaguely correct output --> - <test> - <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/> - <output name="output" format="raw_pepxml"> - <assert_contents> - <has_text text="SQVFQLESTFDV" /> - </assert_contents> - </output> - </test> - </tests> - + <outputs> + <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> + </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/> + <output name="output" format="raw_pepxml"> + <assert_contents> + <has_text text="SQVFQLESTFDV" /> + </assert_contents> + </output> + </test> + </tests> + <help> + Convert X!Tandem results to pepXML + </help> </tool> |
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| diff -r 9d6e0ad4d600 -r 0faaab4f192a tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 20:47:05 2015 -0400 |
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| @@ -0,0 +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="trans_proteomic_pipeline" version="4.8.0"> + <repository changeset_revision="a7273394d858" name="package_tpp_4_8_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |