Mercurial > repos > galaxyp > msconvert
diff msconvert_raw.xml @ 0:ab59b1826345 draft
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 14:00:58 -0400 |
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children | 8e2e7ff2b6bd |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_raw.xml Thu Oct 22 14:00:58 2015 -0400 @@ -0,0 +1,282 @@ +<tool id="msconvert_raw" name="msconvert" 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>