Mercurial > repos > galaxyp > openms_mapalignerposeclustering
changeset 1:40ca4302e603 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
| author | galaxyp |
|---|---|
| date | Mon, 12 Feb 2018 10:28:56 -0500 |
| parents | 70f729e59244 |
| children | 304c13ce9577 |
| files | MapAlignerPoseClustering.xml |
| diffstat | 1 files changed, 26 insertions(+), 6 deletions(-) [+] |
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--- a/MapAlignerPoseClustering.xml Thu Jan 11 18:08:16 2018 -0500 +++ b/MapAlignerPoseClustering.xml Mon Feb 12 10:28:56 2018 -0500 @@ -7,10 +7,24 @@ <expand macro="stdio"/> <expand macro="requirements"/> <command><![CDATA[ + + mkdir -p ./results_trafoxml ./results_out && MapAlignerPoseClustering --in $param_in --out $out --trafo_out $trafo_out + +-in +#for $infile in $param_in: + '$infile' +#end for + +-out +#for $counter,$infile in enumerate($param_in): + ./results_out/${infile.element_identifier}.${infile.extension} +#end for + +-trafo_out +#for $counter,$infile in enumerate($param_in): + ./results_trafoxml/${infile.element_identifier}.trafoxml +#end for -threads "\${GALAXY_SLOTS:-1}" @@ -97,10 +111,11 @@ #end if #end if #end if + ]]> </command> <inputs> - <param name="param_in" type="data" format="mzML,featureXML" label="Input files to align (all must have the same file type)" help="(-in) "/> + <param name="param_in" type="data" format="mzML,featureXML" multiple="true" label="Input files to align (all must have the same file type)" help="(-in) "/> <param name="param_reference_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/> <param name="param_reference_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="(-index) <br>If '0', no explicit reference is set - the algorithm will select a reference"/> <param name="param_algorithm_max_num_peaks_considered" type="integer" min="-1" optional="True" value="1000" label="The maximal number of peaks/features to be considered per map" help="(-max_num_peaks_considered) To use all, set to '-1'"/> @@ -134,8 +149,13 @@ </expand> </inputs> <outputs> - <data name="out" format_source="param_in" metadata_source="param_in" /> - <data name="trafo_out" format_source="param_in" metadata_source="param_in" /> + <collection name="out" type="list"> + <discover_datasets pattern="__designation_and_ext__" directory="results_out"/> + </collection> + + <collection name="trafo_out" type="list"> + <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/> + </collection> </outputs> <help>Corrects retention time distortions between maps using a pose clustering approach.