| Previous changeset 7:3f0cb90824f1 (2013-03-05) Next changeset 9:c04896f31ff7 (2013-06-10) |
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Commit message:
Update |
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modified:
interprophet.xml peptide_prophet.xml pepxml_to_table.xml protein_prophet.xml repository_dependencies.xml tool_dependencies.xml |
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| diff -r 3f0cb90824f1 -r d19a95abf2e4 interprophet.xml --- a/interprophet.xml Tue Mar 05 00:28:22 2013 -0500 +++ b/interprophet.xml Sun Jun 09 08:19:01 2013 -0500 |
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| @@ -1,17 +1,30 @@ <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1"> <requirements> - <requirement type="package" version="1.2.0">galaxy_protk</requirement> + <requirement type="package" version="1.2.2">galaxy_protk</requirement> <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> </requirements> <description>Combine Peptide Prophet results from multiple search engines</description> - <command interpreter="ruby"> + <command interpreter="bash"> + + interprophet_wrapper.sh + + $output + + $use_nss - interprophet_wrapper.rb $output $use_nss $use_nrs $use_nse $use_nsi $use_nsm --minprob $minprob + $use_nrs + + $use_nse + $use_nsi + + $use_nsm + + --minprob $minprob ## Inputs. ${first_input} @@ -29,11 +42,11 @@ <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/> </repeat> - <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--nonss"/> - <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--nonrs"/> - <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--nonse"/> - <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--nonsi"/> - <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--nonsm"/> + <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--no-nss"/> + <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--no-nrs"/> + <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--no-nse"/> + <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--no-nsi"/> + <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--no-nsm"/> <param name="minprob" type="text" label="Minimum threshod probability for reporting results"/> |
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| diff -r 3f0cb90824f1 -r d19a95abf2e4 peptide_prophet.xml --- a/peptide_prophet.xml Tue Mar 05 00:28:22 2013 -0500 +++ b/peptide_prophet.xml Sun Jun 09 08:19:01 2013 -0500 |
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| @@ -1,12 +1,29 @@ <tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.1"> <requirements> - <requirement type="package" version="1.2.0">galaxy_protk</requirement> + <requirement type="package" version="1.2.2">galaxy_protk</requirement> <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> </requirements> <description>Calculate Peptide Prophet statistics on search results</description> - <command interpreter="ruby">peptide_prophet_wrapper.rb ${output} ${input_file} -r $glyco $useicat $phospho $usepi $usert $accurate_mass $no_ntt $no_nmc $use_gamma $use_only_expect $force_fit $allow_alt_instruments $maldi + <command interpreter="bash"> + peptide_prophet_wrapper.sh $output $input_file + + -r + $glyco + $useicat + $phospho + $usepi + $usert + $accurate_mass + $no_ntt + $no_nmc + $use_gamma + $use_only_expect + $force_fit + $allow_alt_instruments + $maldi + </command> <inputs> |
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| diff -r 3f0cb90824f1 -r d19a95abf2e4 pepxml_to_table.xml --- a/pepxml_to_table.xml Tue Mar 05 00:28:22 2013 -0500 +++ b/pepxml_to_table.xml Sun Jun 09 08:19:01 2013 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.1"> <requirements> - <requirement type="package" version="1.2.0">galaxy_protk</requirement> + <requirement type="package" version="1.2.2">galaxy_protk</requirement> </requirements> @@ -10,12 +10,12 @@ <!-- Note .. the input file is assumed to be the first argument --> -<command>rvm 1.9.3@protk-1.2.0 do pepxml_to_table.rb $input_file -o $output</command> +<command>rvm 1.9.3@protk-1.2.2 do pepxml_to_table.rb $input_file -o $output</command> <inputs> - <param name="input_file" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/> + <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/> </inputs> <outputs> |
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| diff -r 3f0cb90824f1 -r d19a95abf2e4 protein_prophet.xml --- a/protein_prophet.xml Tue Mar 05 00:28:22 2013 -0500 +++ b/protein_prophet.xml Sun Jun 09 08:19:01 2013 -0500 |
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| @@ -1,6 +1,6 @@ <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.1"> <requirements> - <requirement type="package" version="1.2.0">galaxy_protk</requirement> + <requirement type="package" version="1.2.2">galaxy_protk</requirement> <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> </requirements> @@ -8,7 +8,27 @@ <!-- Note .. the input file is assumed to be the first argument --> - <command interpreter="ruby">protein_prophet_wrapper.rb --galaxy $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command> + <command interpreter="bash"> + protein_prophet_wrapper.sh + + --galaxy $input_file + + -r + + $iproph + $nooccam + $groupwts + $normprotlen + $logprobs + $confem + $allpeps + $unmapped + $instances + $delude + + --minprob=$minprob + --minindep=$minindep + </command> <inputs> <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/> |
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| diff -r 3f0cb90824f1 -r d19a95abf2e4 repository_dependencies.xml --- a/repository_dependencies.xml Tue Mar 05 00:28:22 2013 -0500 +++ b/repository_dependencies.xml Sun Jun 09 08:19:01 2013 -0500 |
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| @@ -1,10 +1,6 @@ <?xml version="1.0"?> <repositories description="Proteomics datatypes and the TPP"> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="463328a6967f"/> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/> - + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/> </repositories> |
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| diff -r 3f0cb90824f1 -r d19a95abf2e4 tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 05 00:28:22 2013 -0500 +++ b/tool_dependencies.xml Sun Jun 09 08:19:01 2013 -0500 |
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| @@ -1,12 +1,11 @@ <?xml version="1.0"?> <tool_dependency> - - <package name="galaxy_protk" version="1.2.0"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/> + <package name="galaxy_protk" version="1.2.2"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/> + </package> + + <package name="trans_proteomic_pipeline" version="4.6.1"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/> </package> - <package name="trans_proteomic_pipeline" version="4.6.1"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349" /> - </package> - -</tool_dependency> \ No newline at end of file +</tool_dependency> |