Mercurial > repos > galaxyp > thermo_raw_file_converter
view thermo_converter.xml @ 11:19e45916daf9 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 2d431b6ee383f3013d6de3cce64349d51642c33b"
author | galaxyp |
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date | Wed, 21 Apr 2021 12:23:27 +0000 |
parents | b9b385097f13 |
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<tool id="thermo_raw_file_converter" name="Thermo" version="@TOOL_VERSION@+galaxy0" profile="20.05"> <description>RAW file converter</description> <macros> <token name="@TOOL_VERSION@">1.3.4</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">thermorawfileparser</requirement> </requirements> <stdio> <regex match="ERROR" source="both" level="fatal" description="Fatal error"/> </stdio> <version_command><![CDATA[ThermoRawFileParser.sh --version]]></version_command> <command> <![CDATA[ #import re #set $input_name = re.sub('[^\w\-\.]', '_', $input_file.element_identifier.replace(".raw", "") + ".raw") ln -s -f '$input_file' '$input_name' && ThermoRawFileParser.sh --input='$input_name' --output_file='$output' -f=$format_cond.output_format #if $output_metadata_selector != "off": --metadata="$output_metadata_selector" --metadata_output_file='$output_metadata' #end if #if $format_cond.output_format == "0" $format_cond.mgfPrecursor #end if #if $format_cond.output_format in ['1', '2'] $format_cond.zlib_boolean $format_cond.peakpicking_boolean #end if $ignore_instrument_errors_boolean $allDetectors $includeExceptionData #if $msLevel != '' --msLevel="$msLevel" #end if ]]> </command> <inputs> <param argument="--input" name="input_file" type="data" format="thermo.raw" label="Thermo RAW file" help="" optional="False"/> <conditional name="format_cond"> <param argument="--format" name="output_format" type="select" label="Output format"> <option value="0">mgf</option> <option value="1" selected="True">mzml</option> <option value="2">Indexed mzml</option> <!-- <option value="3">Parquet</option> --> </param> <when value="0"> <param argument="--mgfPrecursor" type="boolean" truevalue="--mgfPrecursor" falsevalue="" label="Include precursor scan number in MGF file" help=""/> </when> <when value="1"> <param argument="--noZlibCompression" name="zlib_boolean" type="boolean" truevalue="" falsevalue="-z" checked="true" label="Use zlib compression for the m/z ratios and intensities" help=""/> <param argument="--noPeakPicking" name="peakpicking_boolean" type="boolean" truevalue="" falsevalue="-p" checked="true" label="Use the peak picking provided by the native thermo library" help=""/> </when> <when value="2"> <param argument="--noZlibCompression" name="zlib_boolean" type="boolean" truevalue="" falsevalue="-z" checked="true" label="Use zlib compression for the m/z ratios and intensities" help=""/> <param argument="--noPeakPicking" name="peakpicking_boolean" type="boolean" truevalue="" falsevalue="-p" checked="true" label="Use the peak picking provided by the native thermo library" help=""/> </when> <when value="3"/> </conditional> <param argument="--metadata" name="output_metadata_selector" type="select" label="Output metadata"> <option value="off" selected="True">No</option> <option value="0">json</option> <option value="1">txt</option> </param> <param argument="--ignoreInstrumentErrors" name="ignore_instrument_errors_boolean" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Ignore missing instrument properties" help="If false, it stops the conversion if instrument properties are missing"/> <param argument="--allDetectors" type="boolean" truevalue="--allDetectors" falsevalue="" checked="false" label="Extract additional detector data" help="UV/PDA etc"/> <param argument="--includeExceptionData" type="boolean" truevalue="--includeExceptionData" falsevalue="" label="Include reference and exception data"/> <param argument="--msLevel" type="text" value="" label="Select MS levels " help="(MS1, MS2, etc) included in the output, should be a comma-separated list of integers ( 1,2,3 ) and/or intervals ( 1-3 ), open-end intervals ( 1- ) are allowed"> <sanitizer invalid_char=""> <valid initial="string.digits"> <add value="-"/> <add value=","/> </valid> </sanitizer> </param> </inputs> <outputs> <data name="output" format="mzml" label="${tool.name} on ${on_string}"> <change_format> <when input="format_cond.output_format" value="0" format="mgf"/> <!-- <when input="format_cond.output_format" value="3" format="parquet"/> --> </change_format> </data> <data name="output_metadata" format="txt" label="${tool.name} on ${on_string}: metadata"> <filter>output_metadata_selector != "off"</filter> <change_format> <when input="output_metadata_selector" value="0" format="json"/> </change_format> </data> </outputs> <tests> <!-- mgf test, no metadata --> <test expect_num_outputs="1"> <param name="input_file" value="really_small.raw" ftype="thermo.raw"/> <conditional name="format_cond"> <param name="output_format" value="0"/> <param name="mgfPrecursor" value="true"/> </conditional> <output name="output" ftype="mgf" value="really_small.mgf"> <assert_contents> <has_text text="SCANS=36"/> <has_text text="RTINSECONDS=73.863181104"/> <has_text text="PEPMASS=675.248779296875"/> <has_text text="CHARGE=2+"/> <has_text text="121.3116455 920.2367553711"/> <has_text text="229.2241211 1137.6958007813"/> <has_text text="1577.8967285 1487.9519042969"/> </assert_contents> </output> <assert_command> <has_text text="--mgfPrecursor"></has_text> </assert_command> </test> <!-- mzml test and json metadata --> <test expect_num_outputs="2"> <param name="input_file" value="really_small.raw" ftype="thermo.raw"/> <conditional name="format_cond"> <param name="output_format" value="1"/> </conditional> <param name="output_metadata_selector" value="0"/> <output name="output" file="really_small.mzml" ftype="mzml"/> <output name="output_metadata" value="really_small.json" ftype="json"/> <assert_command> <not_has_text text="--mgfPrecursor"></not_has_text> </assert_command> </test> <!-- mzml test (wo zlib compression and peak picking) and json metadata --> <test expect_num_outputs="2"> <param name="input_file" value="really_small.raw" ftype="thermo.raw"/> <conditional name="format_cond"> <param name="output_format" value="1"/> <param name="zlib_boolean" value="false"/> <param name="peakpicking_boolean" value="false"/> </conditional> <param name="output_metadata_selector" value="0"/> <output name="output" file="really_small_ext.mzml" ftype="mzml"/> <output name="output_metadata" value="really_small.json" ftype="json"/> <assert_command> <not_has_text text="--mgfPrecursor"></not_has_text> <has_text text="-z "></has_text> <has_text text="-p "></has_text> </assert_command> </test> <!-- indexed mzml, txt metadata (+ extra options) --> <test expect_num_outputs="2"> <param name="input_file" value="really_small.raw" ftype="thermo.raw"/> <conditional name="format_cond"> <param name="output_format" value="2"/> </conditional> <param name="output_metadata_selector" value="1"/> <param name="ignore_instrument_errors_boolean" value="true"/> <param name="allDetectors" value="true"/> <param name="includeExceptionData" value="--includeExceptionData"/> <param name="msLevel" value="1"/> <output name="output" value="really_small.indexed_mzML" ftype="mzml"/> <output name="output_metadata" ftype="txt"> <assert_contents> <has_text text="Instrument model=[MS, MS:1000494, Thermo Scientific instrument model, Orbitrap Fusion]"/> <has_text text="Instrument name=Orbitrap Fusion"/> <has_text text="Instrument serial number=[MS, MS:1000529, instrument serial number, FSN10188]"/> <has_text text="Software version=[NCIT, NCIT:C111093, Software Version, 3.1.2412.17]"/> <has_text text="Mass resolution=[MS, MS:1000011, mass resolution, 0.5]"/> <has_text text="Number of scans=101"/> <has_text text="Scan range=1;101"/> <has_text text="Scan start time=0.89"/> <has_text text="Time range=0.89"/> <has_text text="Mass range=120;2000"/> </assert_contents> </output> <assert_command> <not_has_text text="--mgfPrecursor"></not_has_text> <has_text text="-e "/> <has_text text="--allDetectors"/> <has_text text="--includeExceptionData"/> <has_text text="--msLevel="1""/> </assert_command> </test> <!-- parquet test, no metadata <test expect_num_outputs="1"> <param name="input_file" value="really_small.raw" ftype="thermo.raw"/> <conditional name="format_cond"> <param name="output_format" value="3"/> </conditional> <output name="output" ftype="parquet" value="really_small.parquet"/> </test> --> </tests> <help> <![CDATA[ Thermo RAW file converter based on the great `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ project. ]]> </help> <citations> <citation type="doi">10.1021/acs.jproteome.9b00328</citation> </citations> </tool>