Mercurial > repos > galaxyp > msconvert
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
author | galaxyp |
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date | Thu, 22 Oct 2015 17:41:29 -0400 |
parents | ab59b1826345 |
children | 158a71ee5733 |
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<tool id="msconvert_raw" name="msconvert (vendor support)" version="0.3.0"> <description>Convert and/or filter mass spectrometry files (with vendor support on Windows)</description> <requirements> <requirement type="package" version="3.0.9016">proteowizard</requirement> </requirements> <macros> <import>msconvert_macros.xml</import> </macros> <expand macro="msconvertCommand" /> <inputs> <!-- TODO: add Bruker, Waters, Agilent types --> <param format="mzml,mzxml,mz5,mgf,wiff,raw" name="input" type="data" label="Input unrefined MS data" /> <expand macro="msconvertInputParameters" /> </inputs> <expand macro="msconvertOutput" /> <tests> <test> <param name="input" value="small.mzML" /> <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" /> </test> <!-- this data file only has profile MS1, so the result is the same --> <test> <param name="input" value="small.mzML" /> <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" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <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="100" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <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" /> </test> <!-- TODO: how to test gzipped output? <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzXML" /> <param name="mz_encoding" value="32" /> <param name="intensity_encoding" value="32" /> <param name="binary_compression" value="false" /> <param name="gzip_compression" value="true" /> <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="mz_encoding" value="32" /> <param name="intensity_encoding" value="32" /> <param name="binary_compression" value="false" /> <param name="gzip_compression" value="true" /> <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" /> </test>--> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearPic" /> <output name="output" file="small-numpressLP.mzML" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearSlof" /> <output name="output" file="small-numpressLS.mzML" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinear" /> <output name="output" file="small-numpressL.mzML" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressPic" /> <output name="output" file="small-numpressP.mzML" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressSlof" /> <output name="output" file="small-numpressS.mzML" /> </test> <test> <param name="input" value="Rpal_01.mz5" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearPic" /> <param name="use_mzrefinement" value="true" /> <param name="input_ident" value="Rpal_01.pepXML.gz" /> <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="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearPic" /> <param name="charge_state_calculation_method" value="predictor" /> <param name="predictor_overrideExistingCharge" value="true" /> <param name="minMultipleCharge" value="2" /> <param name="maxMultipleCharge" value="5" /> <param name="singleChargeFractionTIC" value="0.95" /> <param name="maxKnownCharge" value="8" /> <output name="output" file="small-chargeStatePredictor.mzML" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearPic" /> <param name="charge_state_calculation_method" value="turbocharger" /> <param name="minCharge" value="1" /> <param name="maxCharge" value="5" /> <param name="precursorsBefore" value="1" /> <param name="precursorsAfter" value="1" /> <param name="halfIsoWidth" value="1.5" /> <param name="defaultMinCharge" value="1" /> <param name="defaultMaxCharge" value="5" /> <output name="output" file="small-turbocharger.mzML" /> </test> <test> <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" /> <param name="output_type" value="mzML" /> <param name="do_etd_filtering" value="true" /> <param name="remove_precursor" value="true" /> <param name="remove_charge_reduced" value="true" /> <param name="remove_neutral_loss" value="false" /> <param name="blanket_removal" value="false" /> <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" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="thresholds_0|threshold_type" value="count" /> <param name="thresholds_0|value" value="100" /> <param name="thresholds_0|orientation" value="most-intense" /> <param name="thresholds_1|threshold_type" value="absolute" /> <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" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <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" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="denoise" value="true" /> <param name="num_peaks" value="10" /> <param name="window_width" value="40" /> <param name="relax" value="false" /> <param name="binary_compression" value="numpressLinearPic" /> <output name="output" file="small-denoise.mzML" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="ms2deisotope" value="true" /> <param name="binary_compression" value="numpressLinearPic" /> <output name="output" file="small-deisotope.mzML" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="activation" value="CID" /> <param name="binary_compression" value="numpressLinearPic" /> <output name="output" file="small-activation.mzML" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="indices_0|from" value="2" /> <param name="indices_0|to" value="4" /> <param name="indices_1|from" value="10" /> <param name="indices_1|to" value="10" /> <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" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <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" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <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" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <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" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <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" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzML" /> <param name="scan_numbers_0|from" value="3" /> <param name="scan_numbers_0|to" value="5" /> <param name="scan_numbers_1|from" value="11" /> <param name="scan_numbers_1|to" value="11" /> <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" /> <!-- the scan numbers here produce the same output as the index test above --> </test> <!--<test> <param name="input" value="small.mzML" /> <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearPic" /> <output name="output" file="small-deisotope-poisson.mzML" /> </test>--> </tests> <help> **What it does** Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available. You can view the original documentation here_. .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html </help> <citations> <citation type="doi">10.1093/bioinformatics/btn323</citation> <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> </citations> </tool>