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comparison msconvert_macros.xml @ 17:ab6c14374bc0 draft default tip

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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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16:545054b15d7c 17:ab6c14374bc0
30 #else 30 #else
31 ln -s '$input' '${basename}' && 31 ln -s '$input' '${basename}' &&
32 #set inputmask = "'"+$basename+"'" 32 #set inputmask = "'"+$basename+"'"
33 #end if 33 #end if
34 34
35 #if $data_processing.precursor_refinement.use_mzrefinement 35 #if $data_processing.precursor_refinement.use_mzrefinement == "true"
36 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext)) 36 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
37 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv' 37 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
38 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' && 38 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
39 #end if 39 #end if
40 40
63 63
64 #if $general_options.scan_summing.do_scan_summing: 64 #if $general_options.scan_summing.do_scan_summing:
65 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol" 65 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"
66 #end if 66 #end if
67 67
68 #if $general_options.multi_run_output.do_multi_run_output: 68 #if $general_options.multi_run_output.do_multi_run_output == "true":
69 #if len($general_options.multi_run_output.run_index_set) > 0 69 #if len($general_options.multi_run_output.run_index_set) > 0
70 --runIndexSet " 70 --runIndexSet "
71 #for $index in $general_options.multi_run_output.run_index_set 71 #for $index in $general_options.multi_run_output.run_index_set
72 [${index.from},${index.to}] 72 [${index.from},${index.to}]
73 #end for 73 #end for
83 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!) 83 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
84 #if $data_processing.peak_picking.pick_peaks 84 #if $data_processing.peak_picking.pick_peaks
85 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" 85 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
86 #end if 86 #end if
87 87
88 #if $data_processing.precursor_refinement.use_mzrefinement 88 #if $data_processing.precursor_refinement.use_mzrefinement == "true"
89 --filter "mzRefiner $input_ident_name 89 --filter "mzRefiner $input_ident_name
90 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels 90 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
91 thresholdScore=$data_processing.precursor_refinement.thresholdScore 91 thresholdScore=$data_processing.precursor_refinement.thresholdScore
92 thresholdValue=$data_processing.precursor_refinement.thresholdValue 92 thresholdValue=$data_processing.precursor_refinement.thresholdValue
93 thresholdStep=$data_processing.precursor_refinement.thresholdStep 93 thresholdStep=$data_processing.precursor_refinement.thresholdStep
227 ## a newline is needed after `#echo ...` therefore the `;'` on the next line 227 ## a newline is needed after `#echo ...` therefore the `;'` on the next line
228 ;' 228 ;'
229 #end if 229 #end if
230 #end if 230 #end if
231 231
232 #if $data_processing.precursor_refinement.use_mzrefinement 232 #if $data_processing.precursor_refinement.use_mzrefinement == "true"
233 && mv '$output_refinement_name' '$output_refinement'; 233 && mv '$output_refinement_name' '$output_refinement';
234 #end if 234 #end if
235 ]]> 235 ]]>
236 </command> 236 </command>
237 </xml> 237 </xml>
558 <when input="output_type" value="ms2" format="ms2" /> 558 <when input="output_type" value="ms2" format="ms2" />
559 <when input="output_type" value="mgf" format="mgf" /> 559 <when input="output_type" value="mgf" format="mgf" />
560 </change_format> 560 </change_format>
561 </data> 561 </data>
562 <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv"> 562 <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
563 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter> 563 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == "true"</filter>
564 </data> 564 </data>
565 <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type} collection"> 565 <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">
566 <filter>general_options['multi_run_output']['do_multi_run_output'] == True</filter> 566 <filter>general_options['multi_run_output']['do_multi_run_output'] == "true"</filter>
567 <discover_datasets pattern="__name_and_ext__" directory="outputs" /> 567 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
568 </collection> 568 </collection>
569 </outputs> 569 </outputs>
570 </xml> 570 </xml>
571 571