Mercurial > repos > jmchilton > johnstestrepo
diff galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert3.xml @ 0:942cec8d04c7 draft
Initial commit.
| author | jmchilton |
|---|---|
| date | Wed, 19 Sep 2012 00:07:16 -0400 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert3.xml Wed Sep 19 00:07:16 2012 -0400 @@ -0,0 +1,311 @@ +<tool id="msconvert3" name="msconvert3" version="0.2.0"> + <!-- BEGIN_VERSION_DEFAULT --> + <description>Convert and filter a mass spec peak list</description> + <!-- END_VERSION_DEFAULT --> + + <command interpreter="python"> + msconvert_wrapper.py + --input=${input} + --output=${output} + ## BEGIN_VERSION_DEFAULT + --fromextension=${input.ext} + ## END_VERSION_DEFAULT + + + --toextension=${output_type} + + #if $settings.settingsType == "full" + --binaryencoding=${settings.binary_encoding} + --mzencoding=${settings.mz_encoding} + --intensityencoding=${settings.intensity_encoding} + --zlib=${settings.zlib} + #end if + + #if $filtering.filtering_use + + #if $filtering.precursor_recalculation.value + --filter "precursorRecalculation" + #end if + + #if $filtering.peak_picking.pick_peaks + --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" + #end if + + #if str($filtering.activation) != "false" + --filter "activation $filtering.activation" + #end if + + #if len($filtering.indices) > 0 + --filter "index + #for $index in $filtering.indices + [${index.from},${index.to}] + #end for + " + #end if + + #if len($filtering.scan_numbers) > 0 + --filter "scanNumber + #for $scanNumber in $filtering.scanNumbers + [${scanNumber.from},${scanNumber.to}] + #end for + " + #end if + + #if $filtering.strip_it.value + --filter "stripIT" + #end if + + #if $filtering.filter_mz_windows.do_filter + --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" + #end if + + + #if $filtering.filter_ms_levels.do_filter + --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "default" + --filter "ETDFilter" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" + --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" + #end if + + ## BEGIN_VERSION_3 + #if str($filtering.ms2deisotope) == "true" + --filter "MS2Deisotope" + #end if + + #if str($filtering.polarity) != "false" + --filter "polarity $filtering.polarity" + #end if + + #if str($filtering.analyzer) != "false" + --filter "analyzer $filtering.analyzer" + #end if + + ## END_VERSION_3 + + #end if + + </command> + + <inputs> + + <!-- BEGIN_VERSION_DEFAULT --> + <conditional name="type"> + <param name="input_type" type="select" label="Input Type"> + <option value="mzml">mzML</option> + <option value="mzxml">mzXML</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <when value="mzml"> + <param format="mzml" name="input" type="data" label="Input mzML"/> + </when> + <when value="mzxml"> + <param format="mzxml" name="input" type="data" label="Input mzXML"/> + </when> + <when value="mgf"> + <param format="mgf" name="input" type="data" label="Input mgf"/> + </when> + <when value="ms2"> + <param format="ms2" name="input" type="data" label="Input ms2"/> + </when> + </conditional> + <!-- END_VERSION_DEFAULT --> + <param name="output_type" type="select" label="Output Type"> + <option value="mzML">mzML (indexed)</option> + <option value="unindexed_mzML">mzML (unindexed)</option> + <option value="mzXML">mzXML (indexed)</option> + <option value="unindexed_mzXML">mzXML (unindexed)</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <conditional name="filtering"> + <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> + + <conditional name="peak_picking"> + <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> + <option value="1">MS1 Only (1)</option> + <option value="2">MS2 Only (2)</option> + <option value="2-">MS2 and on (2-)</option> + <option value="1-">All Levels (1-)</option> + </param> + <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> + </when> + </conditional> + + + <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="HCD">HCD</option> + <!-- BEGIN_VERSION_3 --> + <option>BIRD</option> + <option>ECD</option> + <option>IRMPD</option> + <option>PD</option> + <option>PSD</option> + <option>PQD</option> + <option>SID</option> + <option>SORI</option> + <!-- END_VERSION_3 --> + </param> + + <repeat name="indices" title="Filter Scan Indices"> + <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> + </repeat> + + <repeat name="scan_numbers" title="Filter Scan Numbers"> + <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> + </repeat> + + <conditional name="filter_mz_windows"> + <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> + <when value="false" /> + <when value="true"> + <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> + <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> + </when> + </conditional> + + + <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> + + <conditional name="filter_ms_levels"> + <param name="do_filter" type="boolean" label="Filter MS Levels" /> + <when value="false" /> + <when value="true"> + <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> + </when> + </conditional> + + <conditional name="etd_filtering"> + <param name="do_etd_filtering" type="select" label="ETD Filtering"> + <option value="none" selected="true">none</option> + <option value="default">yes (with default options)</option> + <option value="advanced">yes (show advanced options) </option> + </param> + <when value="none" /> + <when value="default" /> + <when value="advanced"> + <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> + </param> + <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> + <option value="MZ" selected="true">mz</option> + <option value="PPM">ppm</option> + </param> + <param name="remove_precursor" type="select" label="ETD Remove Precursor"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="blanket_removal" type="select" label="ETD Blanket Removal"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + </when> + </conditional> + + + <!-- BEGIN_VERSION_3 --> + <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> + + <param name="polarity" type="select" label="Filter by Polarity"> + <option value="false" selected="true">no</option> + <option value="positive">positive</option> + <option value="negative">negative</option> + </param> + + <param name="analyzer" type="select" label="Filter by Analyzer"> + <option value="false" selected="true">no</option> + <option value="quad">quad</option> + <option value="orbi">orbi</option> + <option value="FT">FT</option> + <option value="IT">IT</option> + <option value="TOF">TOF</option> + </param> + <!-- END_VERSION_3 --> + </when> + </conditional> + + <conditional name="settings"> + <param name="settingsType" type="select" label="Advanced Settings" help=""> + <option value="default">Use Defaults</option> + <option value="full">Full Parameter List</option> + </param> + <when value="default" /> + <when value="full"> + <param type="select" name="binary_encoding" label="Binary Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="mz_encoding" label="m/z Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> + <option value="64">64</option> + <option value="32" selected="true">32</option> + </param> + <param type="boolean" name="zlib" label="Use zlib"> + </param> + </when> + </conditional> + + + </inputs> + <outputs> + <data format="mzml" name="output"> + <change_format> + <when input="output_type" value="mzxml" format="mzxml" /> + <when input="output_type" value="unindexed_mzxml" format="mzxml" /> + <when input="output_type" value="ms2" format="ms2" /> + <when input="output_type" value="mgf" format="mgf" /> + </change_format> + </data> + </outputs> + + <requirements> + <requirement type="package">proteowizard</requirement> + </requirements> + + <help> +**What it does** + +Converts between various mass spectrometry peak list representations. 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 + +------ + +**Citation** + +For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert + + </help> +</tool>