Mercurial > repos > galaxyp > msconvert
diff msconvert_macros.xml @ 17:ab6c14374bc0 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6
| author | galaxyp |
|---|---|
| date | Thu, 15 Aug 2024 16:19:28 +0000 |
| parents | 545054b15d7c |
| children |
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--- a/msconvert_macros.xml Sun Mar 24 11:13:43 2024 +0000 +++ b/msconvert_macros.xml Thu Aug 15 16:19:28 2024 +0000 @@ -32,7 +32,7 @@ #set inputmask = "'"+$basename+"'" #end if - #if $data_processing.precursor_refinement.use_mzrefinement + #if $data_processing.precursor_refinement.use_mzrefinement == "true" #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext)) #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv' ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' && @@ -65,7 +65,7 @@ --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol" #end if - #if $general_options.multi_run_output.do_multi_run_output: + #if $general_options.multi_run_output.do_multi_run_output == "true": #if len($general_options.multi_run_output.run_index_set) > 0 --runIndexSet " #for $index in $general_options.multi_run_output.run_index_set @@ -85,7 +85,7 @@ --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" #end if - #if $data_processing.precursor_refinement.use_mzrefinement + #if $data_processing.precursor_refinement.use_mzrefinement == "true" --filter "mzRefiner $input_ident_name msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels thresholdScore=$data_processing.precursor_refinement.thresholdScore @@ -229,7 +229,7 @@ #end if #end if - #if $data_processing.precursor_refinement.use_mzrefinement + #if $data_processing.precursor_refinement.use_mzrefinement == "true" && mv '$output_refinement_name' '$output_refinement'; #end if ]]> @@ -560,10 +560,10 @@ </change_format> </data> <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv"> - <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter> + <filter>data_processing['precursor_refinement']['use_mzrefinement'] == "true"</filter> </data> <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type} collection"> - <filter>general_options['multi_run_output']['do_multi_run_output'] == True</filter> + <filter>general_options['multi_run_output']['do_multi_run_output'] == "true"</filter> <discover_datasets pattern="__name_and_ext__" directory="outputs" /> </collection> </outputs>