Mercurial > repos > iracooke > tpp_prophets
diff interprophet.xml @ 15:0746a2ae9e04 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author | iracooke |
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date | Tue, 20 Oct 2015 20:45:24 -0400 |
parents | d90c8bc10a9c |
children | 1b86e378de37 |
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--- a/interprophet.xml Thu Mar 26 19:55:19 2015 -0400 +++ b/interprophet.xml Tue Oct 20 20:45:24 2015 -0400 @@ -1,59 +1,71 @@ -<tool id="proteomics_search_interprophet_1" name="InterProphet" 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> - </requirements> - - - <description>Combine Peptide Prophet results from multiple search engines</description> - - <command>interprophet.rb --galaxy +<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.1"> + <description>Combine Peptide Prophet results from multiple search engines</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> +<![CDATA[ + interprophet.rb --galaxy + #if str( $input_type.type ) == "files": + #for $pepxml_file in $input_type.pepxml_files: + ${pepxml_file} + #end for + #else + #for $list_item in $input_type.pepxml_list: + ${list_item} + #end for + #for $extra_list_holder in $input_type.extra_pepxml_lists: + #for $list_item in $extra_list_holder.extra_list: + ${list_item} + #end for + #end for + #end if - -o interprophet_output.pep.xml - - $use_nss - - $use_nrs - - $use_nse - - $use_nsi - - $use_nsm - - --p-thresh $p_thresh + -o interprophet_output.pep.xml + $use_nss + $use_nrs + $use_nse + $use_nsi + $use_nsm + --p-thresh $p_thresh + --threads "\${GALAXY_SLOTS:-12}" - --threads $threads - -#for $pepxml_file in $pepxml_files: - ${pepxml_file} -#end for - - </command> - - - <inputs> - - <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> +]]> + </command> + <inputs> - <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" 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="" 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="" 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="" 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="" falsevalue="--no-nsm"/> - - <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + <conditional name="input_type"> + <param name="type" type="select" label="Input Type"> + <option value="files" selected="true">Datasets</option> + <option value="collections">Collections</option> + </param> + <when value="files"> + <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> + </when> + <when value="collections"> + <param name="pepxml_list" type="data_collection" multiple="true" collection_type="list" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> + <repeat name="extra_pepxml_lists" title="Additional PepXML Collections" > + <param name="extra_list" type="data_collection" multiple="true" collection_type="list" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> + </repeat> + </when> + </conditional> - <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/> - - </inputs> - <outputs> - <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/> - </outputs> + <!-- <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> --> - <help> + <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" 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="" 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="" 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="" 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="" falsevalue="--no-nsm"/> + <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + + </inputs> + <outputs> + <data format="interprophet_pepxml" name="output" from_work_dir="interprophet_output.pep.xml"/> + </outputs> + <help> **What it does** @@ -67,6 +79,5 @@ Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011). - </help> - + </help> </tool>