Mercurial > repos > galaxyp > msconvert
diff msconvert_macros.xml @ 15:6153e8ada1ee draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
author | galaxyp |
---|---|
date | Mon, 30 Nov 2020 16:01:10 +0000 |
parents | 3cf310697624 |
children | 545054b15d7c |
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--- a/msconvert_macros.xml Mon Nov 16 17:25:12 2020 +0000 +++ b/msconvert_macros.xml Mon Nov 30 16:01:10 2020 +0000 @@ -1,7 +1,6 @@ <macros> - <token name="@VERSION@">3.0.19052</token> - <token name="@FULL_VERSION@">@VERSION@-089e81090</token> - + <token name="@VERSION@">3.0.20287</token> + <token name="@FULL_VERSION@">@VERSION@-769529fa4</token> <xml name="msconvertCommand"> <command detect_errors="exit_code"> <![CDATA[ @@ -39,18 +38,17 @@ ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' && #end if - - CAN_SUDO=\$(sudo -n -l 2> /dev/null; echo \$?) && + CAN_SUDO=\$(sudo -n -l > /dev/null 2> /dev/null; echo $?) && if [ "\$CAN_SUDO" -eq "0" ]; then - uid=`id -u` && - gid=`id -g` && - WINE="wine64_anyuser"; + 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); + 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} @@ -214,21 +212,25 @@ #if $general_options.multi_run_output.do_multi_run_output == 'false': --outfile '${os.path.splitext($basename)[0]}' - && - if [ "\$CAN_SUDO" -eq "0" ]; then - sudo chown \$uid:\$gid 'outputs/${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 + #end if + && + if [ "\$CAN_SUDO" -eq "0" ]; then + sudo chown -R \$uid:\$gid './'; + fi + #if $general_options.multi_run_output.do_multi_run_output == 'false': + && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' #else - && ls -la outputs/ + ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file + ## TODO this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803 + #if $output_type == 'mzML' or $output_type == 'mzXML' + && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower() + ## a newline is needed after `#echo ...` therefore the `;'` on the next line +;' + #end if #end if #if $data_processing.precursor_refinement.use_mzrefinement - && if [ "\$CAN_SUDO" -ne "0" ]; then - mv '$output_refinement_name' '$output_refinement'; - fi + && mv '$output_refinement_name' '$output_refinement'; #end if ]]> </command> @@ -543,13 +545,13 @@ <xml name="msconvert_tests"> <test> - <param name="input" value="small.mzML" /> + <param name="input" value="small.mzML" ftype="mzml" /> <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" /> + <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" /> </test> <test> <param name="input" value="small.RAW" ftype="thermo.raw" /> @@ -558,47 +560,47 @@ <param name="pick_peaks" value="true" /> <param name="pick_peaks_algorithm" value="vendor" /> <param name="pick_peaks_ms_levels" value="1-" /> - <output name="output" file="small-peakpicking-vendor-allMS.mzML" lines_diff="4" /> + <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" /> </test> <test> - <param name="input" value="ThyroglobMRM000003.d.tar" /> + <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="combineIonMobilitySpectra" value="true" /> <param name="do_scan_summing" value="true" /> - <output name="output" file="ThyroglobMRM000003.mzML" lines_diff="4" /> + <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" /> </test> <test> - <param name="input" value="MassLynxTest.raw.tar" /> + <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <output name="output" file="MassLynxTest.mzML" lines_diff="4" /> + <output name="output" file="MassLynxTest.mzML" ftype="mzml" lines_diff="4" /> </test> <test> - <param name="input" value="AgilentMassHunterTest.d.tar" /> + <param name="input" value="AgilentMassHunterTest.d.tar" ftype="agilentmasshunter.d.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzXML" /> - <output name="output" file="AgilentMassHunterTest.mzXML" lines_diff="4" /> + <output name="output" file="AgilentMassHunterTest.mzXML" ftype="mzxml" lines_diff="4" /> </test> <test> - <param name="input" value="BrukerBafTest.d.tar" /> + <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="pick_peaks" value="true" /> <param name="pick_peaks_algorithm" value="vendor" /> <param name="pick_peaks_ms_levels" value="1-" /> - <output name="output" file="BrukerBafTest.mzML" lines_diff="4" /> + <output name="output" file="BrukerBafTest.mzML" ftype="mzml" lines_diff="4" /> </test> <test> - <param name="input" value="SciexTest.wiff.tar" /> + <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="do_multi_run_output" value="false" /> <param name="runIndexSet" value="0" /> - <output name="output" file="SciexTest-HPINalone.mzML" lines_diff="4" /> + <output name="output" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" /> </test> <test> - <param name="input" value="SciexTest.wiff.tar" /> + <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzXML" /> <param name="do_multi_run_output" value="false" /> @@ -606,10 +608,10 @@ <param name="indices_0|from" value="0" /> <param name="indices_0|to" value="499" /> <param name="srmAsSpectra" value="true" /> - <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" lines_diff="4" /> + <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" /> </test> <test> - <param name="input" value="SciexTest.wiff.tar" /> + <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzXML" /> <param name="do_multi_run_output" value="false" /> @@ -617,56 +619,56 @@ <param name="indices_0|from" value="0" /> <param name="indices_0|to" value="499" /> <param name="srmAsSpectra" value="true" /> - <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" lines_diff="4" /> + <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" /> </test> <test> - <param name="input" value="SciexTest.wiff.tar" /> + <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="do_multi_run_output" value="true" /> <param name="run_index_set_0|from" value="0" /> <param name="run_index_set_0|to" value="1" /> <output_collection name="multi_run_output_list" type="list"> - <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" /> - <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" /> + <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" /> + <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" /> </output_collection> </test> <test> - <param name="input" value="SciexTest.wiff.tar" /> + <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="do_multi_run_output" value="true" /> <output_collection name="multi_run_output_list" type="list"> - <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" /> - <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" /> + <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" /> + <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" /> </output_collection> </test> <!-- this data file only has profile MS1, so the result is the same --> <test> - <param name="input" value="small.mzML" /> + <param name="input" value="small.mzML" ftype="mzml" /> <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" /> + <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mz5" /> <param name="mz_encoding" value="64" /> <param name="intensity_encoding" value="64" /> - <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" /> + <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzXML" /> <param name="mz_encoding" value="32" /> <param name="intensity_encoding" value="32" /> - <output name="output" file="small-zlib-32.mzXML" lines_diff="6" /> + <output name="output" file="small-zlib-32.mzXML" ftype="mzxml" lines_diff="6" /> </test> <!-- TODO: how to test gzipped output? <test> @@ -689,47 +691,47 @@ </test>--> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-numpressLP.mzML" lines_diff="114" /> + <output name="output" file="small-numpressLP.mzML" ftype="mzml" lines_diff="114" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearSlof" /> - <output name="output" file="small-numpressLS.mzML" lines_diff="114" /> + <output name="output" file="small-numpressLS.mzML" ftype="mzml" lines_diff="114" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinear" /> - <output name="output" file="small-numpressL.mzML" lines_diff="114" /> + <output name="output" file="small-numpressL.mzML" ftype="mzml" lines_diff="114" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressPic" /> - <output name="output" file="small-numpressP.mzML" lines_diff="114" /> + <output name="output" file="small-numpressP.mzML" ftype="mzml" lines_diff="114" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressSlof" /> - <output name="output" file="small-numpressS.mzML" lines_diff="114" /> + <output name="output" file="small-numpressS.mzML" ftype="mzml" lines_diff="114" /> </test> <test> - <param name="input" value="Rpal_01.mz5" /> + <param name="input" value="Rpal_01.mz5" ftype="mz5" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearPic" /> @@ -737,12 +739,12 @@ <param name="input_ident" value="Rpal_01.pepXML" /> <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" /> + <output name="output" file="Rpal_01-mzRefinement.mzML" ftype="mzml" compare="sim_size" delta="0" /> + <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearPic" /> @@ -752,10 +754,10 @@ <param name="maxMultipleCharge" value="5" /> <param name="singleChargeFractionTIC" value="0.95" /> <param name="maxKnownCharge" value="8" /> - <output name="output" file="small-chargeStatePredictor.mzML" lines_diff="114" /> + <output name="output" file="small-chargeStatePredictor.mzML" ftype="mzml" lines_diff="114" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearPic" /> @@ -767,10 +769,10 @@ <param name="halfIsoWidth" value="1.5" /> <param name="defaultMinCharge" value="1" /> <param name="defaultMaxCharge" value="5" /> - <output name="output" file="small-turbocharger.mzML" lines_diff="114" /> + <output name="output" file="small-turbocharger.mzML" ftype="mzml" lines_diff="114" /> </test> <test> - <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" /> + <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="do_etd_filtering" value="true" /> @@ -781,10 +783,10 @@ <param name="matching_tolerance" value="50" /> <param name="matching_tolerance_units" value="ppm" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" /> + <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="thresholds_0|threshold_type" value="count" /> @@ -794,20 +796,20 @@ <param name="thresholds_1|value" value="1" /> <param name="thresholds_1|orientation" value="most-intense" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-threshold.mzML" lines_diff="114" /> + <output name="output" file="small-threshold.mzML" lines_diff="114" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="do_mzwindow_filter" value="true" /> <param name="mz_window_from" value="420" /> <param name="mz_window_to" value="840" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-mzWindow.mzML" lines_diff="114" /> + <output name="output" file="small-mzWindow.mzML" lines_diff="114" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="denoise" value="true" /> @@ -815,26 +817,26 @@ <param name="window_width" value="40" /> <param name="relax" value="false" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-denoise.mzML" lines_diff="114" /> + <output name="output" file="small-denoise.mzML" lines_diff="114" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="ms2deisotope" value="true" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-deisotope.mzML" lines_diff="114" /> + <output name="output" file="small-deisotope.mzML" lines_diff="114" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="activation" value="CID" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-activation.mzML" lines_diff="114" /> + <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="indices_0|from" value="2" /> @@ -844,44 +846,44 @@ <param name="indices_2|from" value="13" /> <param name="indices_2|to" value="15" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-index-filter.mzML" lines_diff="32" /> + <output name="output" file="small-index-filter.mzML" lines_diff="32" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="strip_it" value="true" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-strip-it.mzML" lines_diff="100" /> + <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="do_ms_level_filter" value="true" /> <param name="ms_level_from" value="2" /> <param name="ms_level_to" value="2" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" /> + <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="polarity" value="positive" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-polarity-filter.mzML" lines_diff="114" /> + <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="analyzer" value="IT" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" /> + <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" /> </test> <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="scan_numbers_0|from" value="3" /> @@ -891,7 +893,7 @@ <param name="scan_numbers_2|from" value="14" /> <param name="scan_numbers_2|to" value="16" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above --> + <output name="output" file="small-index-filter.mzML" lines_diff="86" ftype="mzml"/> <!-- the scan numbers here produce the same output as the index test above --> </test> <!--<test> <param name="input" value="small.mzML" />