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Fix boolean to select bugs in msconvert #755

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merged 2 commits into from
Jul 26, 2024
Merged

Fix boolean to select bugs in msconvert #755

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e06e673
Fix boolean to select bugs in msconvert
mvdbeek Apr 12, 2024
e980a63
Merge branch 'master' into fix_boolean_to_select_transition
bgruening Apr 27, 2024
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2 changes: 1 addition & 1 deletion tools/msconvert/msconvert.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="msconvert" name="msconvert" version="@VERSION@.3">
<tool id="msconvert" name="msconvert" version="@VERSION@.4">
<description>Convert and/or filter mass spectrometry files</description>
<macros>
<import>msconvert_macros.xml</import>
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12 changes: 6 additions & 6 deletions tools/msconvert/msconvert_macros.xml
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Expand Up @@ -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' &&
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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' '$output_refinement';
#end if
]]>
Expand Down Expand Up @@ -560,10 +560,10 @@
</change_format>
</data>
<data format="tsv" name="output_refinement" label="${($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>
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