msconvert: msconvert_macros.xml comparison

comparison msconvert_macros.xml @ 14:3cf310697624 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"

author	galaxyp
date	Mon, 16 Nov 2020 17:25:12 +0000
parents	9b61227976d6
children	6153e8ada1ee

comparison

equal deleted inserted replaced

-:9b61227976d6
+:3cf310697624
 <macros>
 <token name="@VERSION@">3.0.19052</token>
 <token name="@FULL_VERSION@">@VERSION@-089e81090</token>
 <xml name="msconvertCommand">
 <command detect_errors="exit_code">
 <![CDATA[
 #import re
 #set $ext = $input.ext
 #set input_ident_name = ".".join((os.path.splitext($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' &&
 #end if
-uid=`id -u` &&
-gid=`id -g` &&
+CAN_SUDO=\$(sudo -n -l 2> /dev/null; echo \$?) &&
+if [ "\$CAN_SUDO" -eq "0" ]; then
-wine64_anyuser msconvert ${inputmask}
+uid=`id -u` &&
+gid=`id -g` &&
+WINE="wine64_anyuser";
+else
+WINE="wine64" &&
+## create a writable copy of wine prefix (since copying fails for some html
+## stderr and exit code is swallowed)
+export WINEPREFIX=\$(mktemp -d) &&
+(cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true);
+fi
+&&
+\$WINE msconvert ${inputmask}
 --outdir outputs
 --${output_type}
+$general_options.combineIonMobilitySpectra
-#if $general_options.combineIonMobilitySpectra:
+$general_options.simAsSpectra
---combineIonMobilitySpectra
+$general_options.srmAsSpectra
-#end if
+$general_options.acceptZeroLengthSpectra
+$general_options.ignoreUnknownInstrumentError
-#if $general_options.simAsSpectra:
---simAsSpectra
-#end if
-#if $general_options.srmAsSpectra:
---srmAsSpectra
-#end if
-#if $general_options.acceptZeroLengthSpectra:
---acceptZeroLengthSpectra
-#end if
-#if $general_options.ignoreUnknownInstrumentError:
---ignoreUnknownInstrumentError
-#end if
 #if $general_options.scan_summing.do_scan_summing:
 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"
 #end if
 #end if
 #if str($filtering.analyzer) != "false"
 --filter "analyzer $filtering.analyzer"
 #end if
 ## OUTPUT ENCODING
 #set $mz_encoding = str($settings.mz_encoding)
 #set $intensity_encoding = str($settings.intensity_encoding)
 #if $mz_encoding == $intensity_encoding
 #if $mz_encoding == "64"
 --64
 --gzip
 #end if
 #if $general_options.multi_run_output.do_multi_run_output == 'false':
 --outfile '${os.path.splitext($basename)[0]}'
-&& sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' && sudo chown \$uid:\$gid '${output}'
+&&
+if [ "\$CAN_SUDO" -eq "0" ]; then
+sudo chown \$uid:\$gid 'outputs/${os.path.splitext($basename)[0]}.${output_type}' &&
+sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}';
+else
+mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}';
+fi
 #else
-&& sudo chown \$uid:\$gid 'outputs' -R
 && ls -la outputs/
 #end if
 #if $data_processing.precursor_refinement.use_mzrefinement
-&& sudo mv '$output_refinement_name' '$output_refinement' && sudo chown \$uid:\$gid '$output_refinement'
+&& if [ "\$CAN_SUDO" -ne "0" ]; then
+mv '$output_refinement_name' '$output_refinement';
+fi
 #end if
 ]]>
 </command>
 </xml>
 <option value="mzXML">mzXML</option>
 <option value="mgf">mgf</option>
 <option value="ms2">ms2</option>
 </param>
 <section name="data_processing" title="Data Processing Filters">
 <conditional name="peak_picking">
 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
 <when value="false" />
 <when value="true">
 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
 </section>
 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
 <param name="activation" type="select" label="Filter by Activation">
 <option value="false" selected="true">no</option>
 <option value="ETD">ETD</option>
 <option value="CID">CID</option>
 <option value="SA">SA</option>
 <option value="TOF">Time of flight</option>
 </param>
 </section>
 <section name="general_options" title="General Options">
-<param argument="--combineIonMobilitySpectra" type="boolean" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." />
+<param argument="--combineIonMobilitySpectra" type="boolean" truevalue="--combineIonMobilitySpectra" falsevalue="" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." />
 <conditional name="scan_summing">
 <param name="do_scan_summing" type="boolean" truevalue="true" falsevalue="false" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR" />
 <when value="false" />
 <when value="true">
 <param name="scanTimeTol" type="float" label="Scan time tolerance" value="10.0" min="0" optional="true" help="Spectra with scan times with a difference less than this tolerance (in seconds) are summed together." />
 <param name="ionMobilityTol" type="float" label="Ion mobility tolerance" value="0.01" min="0" optional="true" help="Spectra with ion mobility values with a difference less than this tolerance are summed together. Only relevant for ion mobility spectra." />
 </when>
 </conditional>
-<param argument="--simAsSpectra" type="boolean" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" />
+<param argument="--simAsSpectra" type="boolean" truevalue="--simAsSpectra" falsevalue="" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" />
-<param argument="--srmAsSpectra" type="boolean" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" />
+<param argument="--srmAsSpectra" type="boolean" truevalue="--srmAsSpectra" falsevalue=""  label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" />
-<param argument="--acceptZeroLengthSpectra" type="boolean" label="Accept zero-length spectra" help="Some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file" />
+<param argument="--acceptZeroLengthSpectra" type="boolean" truevalue="--acceptZeroLengthSpectra" falsevalue=""  label="Accept zero-length spectra" help="Some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file" />
-<param argument="--ignoreUnknownInstrumentError" type="boolean" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" />
+<param argument="--ignoreUnknownInstrumentError" type="boolean" truevalue="--ignoreUnknownInstrumentError" falsevalue=""  label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" />
 <conditional name="multi_run_output">
 <param name="do_multi_run_output" type="boolean" truevalue="true" falsevalue="false" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)" />
 <when value="false">
 <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" />
 <option value="numpressSlof">numpressSlof only</option>
 </param>
 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
 </section>
 </xml>
 <xml name="msconvertOutput">
 <outputs>
 <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" >
 <filter>general_options['multi_run_output']['do_multi_run_output'] == False</filter>
 <change_format>
 <param name="license_agreement" value="true" />
 <param name="output_type" value="mzML" />
 <param name="pick_peaks" value="true" />
 <param name="pick_peaks_algorithm" value="cwt" />
 <param name="pick_peaks_ms_levels" value="1" />
 <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" />
 </test>
 <test>
 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
 <param name="license_agreement" value="true" />
 <param name="output_type" value="mz5" />
 <param name="thresholdScore" value="mvh" />
 <param name="thresholdValue" value="40-" />
 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
 </test>
 <test>
 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
 <param name="license_agreement" value="true" />
 <param name="output_type" value="mzML" />
 <param name="binary_compression" value="numpressLinearPic" />

Mercurial > repos > galaxyp > msconvert

comparison msconvert_macros.xml @ 14:3cf310697624 draft