Repository 'msconvert'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert

Changeset 11:cc5ccfa8ee28 (2019-02-28)
Previous changeset 10:9d5de24e6ef7 (2019-02-23) Next changeset 12:9ec469ff191a (2019-03-22)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d
modified:
msconvert_macros.xml
removed:
msconvert_macros.xml.orig
b
diff -r 9d5de24e6ef7 -r cc5ccfa8ee28 msconvert_macros.xml
--- a/msconvert_macros.xml Sat Feb 23 06:25:48 2019 -0500
+++ b/msconvert_macros.xml Thu Feb 28 14:14:44 2019 -0500
[
@@ -9,19 +9,30 @@
     #set $ext = $input.ext
 
     ## sanitize display name for use as temp filename
-    #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.element_identifier)
+    #set basename = $re.sub(r'[^\w ,.\-+]','_',$input.element_identifier)
 
     #if $ext == 'wiff':
       ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' &&
       ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' &&
+      #set inputmask = "'"+$basename+"'"
     #elif $ext.endswith('tar'):
       ln -s '$input' '${basename}' &&
       tar xf '${basename}' &&
       #set basename = $os.path.splitext($basename)[0]
+      #if $ext.startswith('waters'):
+        #set inputmask = '*.raw'
+      #elif $ext.startswith('agilent') or $ext.startswith('bruker'):
+        #set inputmask = '*.d'
+      #elif $ext.startswith('wiff'):
+        #set inputmask = '*.wiff *.wiff2'
+      #else
+        #raise RuntimeError("Unrecognized type of tar (${ext})")
+      #end if
     #else
       ln -s '$input' '${basename}' &&
+      #set inputmask = "'"+$basename+"'"
     #end if
-    
+
     #if $data_processing.precursor_refinement.use_mzrefinement
       #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
       #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
@@ -31,7 +42,7 @@
     uid=`id -u` &&
     gid=`id -g` &&
 
-    wine64_anyuser msconvert '${basename}'
+    wine64_anyuser msconvert ${inputmask}
     --outdir outputs
     --${output_type}
 
b
diff -r 9d5de24e6ef7 -r cc5ccfa8ee28 msconvert_macros.xml.orig
--- a/msconvert_macros.xml.orig Sat Feb 23 06:25:48 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,897 +0,0 @@\n-<macros>\n-  <token name="@VERSION@">3.0.19052</token>\n-  <token name="@FULL_VERSION@">@VERSION@-089e81090</token>\n-  \n-  <xml name="msconvertCommand">\n-    <command detect_errors="exit_code">\n-<![CDATA[\n-    #import re\n-    #set $ext = $input.ext\n-\n-    ## sanitize display name for use as temp filename\n-    #set basename = $re.sub(r\'[^\\w\\.\\-\\+]\',\'_\',$input.element_identifier)\n-\n-    #if $ext == \'wiff\':\n-      ln -s \'${input.extra_files_path}/wiff\' \'${basename}.wiff\' &&\n-      ln -s \'${input.extra_files_path}/wiff_scan\' \'${basename}.wiff.scan\' &&\n-    #elif $ext.endswith(\'tar\'):\n-      ln -s \'$input\' \'${basename}\' &&\n-      tar xf \'${basename}\' &&\n-      #set basename = $os.path.splitext($basename)[0]\n-    #else\n-      ln -s \'$input\' \'${basename}\' &&\n-    #end if\n-    \n-    #if $data_processing.precursor_refinement.use_mzrefinement\n-      #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))\n-      #set output_refinement_name = os.path.splitext($basename)[0] + \'.mzRefinement.tsv\'\n-      ln -s \'$data_processing.precursor_refinement.input_ident\' \'$input_ident_name\' &&\n-    #end if\n-\n-    uid=`id -u` &&\n-    gid=`id -g` &&\n-\n-    wine64_anyuser msconvert \'${basename}\'\n-    --outdir outputs\n-    --${output_type}\n-\n-    #if $general_options.combineIonMobilitySpectra:\n-    --combineIonMobilitySpectra\n-    #end if\n-\n-    #if $general_options.simAsSpectra:\n-    --simAsSpectra\n-    #end if\n-\n-    #if $general_options.srmAsSpectra:\n-    --srmAsSpectra\n-    #end if\n-\n-    #if $general_options.acceptZeroLengthSpectra:\n-    --acceptZeroLengthSpectra\n-    #end if\n-\n-    #if $general_options.ignoreUnknownInstrumentError:\n-    --ignoreUnknownInstrumentError\n-    #end if\n-\n-    #if $general_options.scan_summing.do_scan_summing:\n-      --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"\n-    #end if\n-\n-    #if $general_options.multi_run_output.do_multi_run_output:\n-      #if len($general_options.multi_run_output.run_index_set) > 0\n-        --runIndexSet "\n-        #for $index in $general_options.multi_run_output.run_index_set\n-          [${index.from},${index.to}]\n-        #end for\n-        "\n-      #end if\n-    #else\n-      --runIndexSet $general_options.multi_run_output.runIndexSet\n-    #end if\n-\n-    ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests\n-    --stripLocationFromSourceFiles\n-\n-    ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)\n-      #if $data_processing.peak_picking.pick_peaks\n-        --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"\n-      #end if\n-\n-      #if $data_processing.precursor_refinement.use_mzrefinement\n-      --filter "mzRefiner $input_ident_name\n-        msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels\n-        thresholdScore=$data_processing.precursor_refinement.thresholdScore\n-        thresholdValue=$data_processing.precursor_refinement.thresholdValue\n-        thresholdStep=$data_processing.precursor_refinement.thresholdStep\n-        maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"\n-      #end if\n-\n-      #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"\n-      --filter "chargeStatePredictor\n-        overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge\n-        minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge\n-        maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge\n-        singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC\n-        maxKnownCharge='..b'param name="indices_1|to" value="10" />\n-      <param name="indices_2|from" value="13" />\n-      <param name="indices_2|to" value="15" />\n-      <param name="binary_compression" value="numpressLinearPic" />\n-      <output name="output" file="small-index-filter.mzML" lines_diff="32" />\n-    </test>\n-    <test>\n-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n-      <param name="license_agreement" value="true" />\n-      <param name="output_type" value="mzml" />\n-      <param name="strip_it" value="true" />\n-      <param name="binary_compression" value="numpressLinearPic" />\n-      <output name="output" file="small-strip-it.mzML" lines_diff="100" />\n-    </test>\n-    <test>\n-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n-      <param name="license_agreement" value="true" />\n-      <param name="output_type" value="mzml" />\n-      <param name="do_ms_level_filter" value="true" />\n-      <param name="ms_level_from" value="2" />\n-      <param name="ms_level_to" value="2" />\n-      <param name="binary_compression" value="numpressLinearPic" />\n-      <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />\n-    </test>\n-    <test>\n-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n-      <param name="license_agreement" value="true" />\n-      <param name="output_type" value="mzml" />\n-      <param name="polarity" value="positive" />\n-      <param name="binary_compression" value="numpressLinearPic" />\n-      <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />\n-    </test>\n-    <test>\n-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n-      <param name="license_agreement" value="true" />\n-      <param name="output_type" value="mzml" />\n-      <param name="analyzer" value="IT" />\n-      <param name="binary_compression" value="numpressLinearPic" />\n-      <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />\n-    </test>\n-    <test>\n-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n-      <param name="license_agreement" value="true" />\n-      <param name="output_type" value="mzml" />\n-      <param name="scan_numbers_0|from" value="3" />\n-      <param name="scan_numbers_0|to" value="5" />\n-      <param name="scan_numbers_1|from" value="11" />\n-      <param name="scan_numbers_1|to" value="11" />\n-      <param name="scan_numbers_2|from" value="14" />\n-      <param name="scan_numbers_2|to" value="16" />\n-      <param name="binary_compression" value="numpressLinearPic" />\n-      <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->\n-    </test>\n-    <!--<test>\n-      <param name="input" value="small.mzML" />\n-      <param name="output_type" value="mzml" />\n-      <param name="binary_compression" value="numpressLinearPic" />\n-      <output name="output" file="small-deisotope-poisson.mzML" />\n-    </test>-->\n-  </xml>\n-  <xml name="msconvert_help">\n-**What it does**\n-\n-Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.\n-\n-You can view the original documentation here_.\n-\n-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n-  </xml>\n-\n-  <xml name="citations">\n-    <citations>\n-        <citation type="doi">10.1093/bioinformatics/btn323</citation>\n-        <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},\n-                                      year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->\n-    </citations>\n-  </xml>\n-\n-</macros>\n'