comparison thermo_converter.xml @ 9:92ac8e086317 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"

8:26c6706bfb07

<tool id="thermo_raw_file_converter" name="Thermo" version="1.2.3+galaxy0">
    <description>RAW file converter</description>
    <requirements>
        <requirement type="package" version="1.2.3">thermorawfileparser</requirement>
    </requirements>
    <command>
<![CDATA[
#import re

mkdir ./raws_folder &&
mkdir ./output_folder &&
#for $input_raw in $input_files:
    #set $input_name = re.sub('[^\w\-\.]', '_',$input_raw.element_identifier.split('/')[-1].replace(".raw", "") + ".raw")
    ln -s -f '${input_raw}' './raws_folder/${input_name}' &&
#end for

ThermoRawFileParser.sh
    -d=./raws_folder
    -o=./output_folder
    -f=$output_format
    #if $output_metadata_selector != "off":
        --metadata="${output_metadata_selector}"
    #end if
    $zlib_boolean
    $peakpicking_boolean
    $ignore_instrument_errors_boolean

]]>
    </command>
    <inputs>
        <param name="input_files" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true"
          optional="False" />

        <param 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>
        </param>

        <param name="zlib_boolean" type="boolean" truevalue="" falsevalue="-z" checked="true"
            label="Use zlib compression for the m/z ratios and intensities" help="" />

        <param name="peakpicking_boolean" type="boolean" truevalue="" falsevalue="-p" checked="true"
            label="Use the peak picking provided by the native thermo library" help="" />

        <param 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 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>

    </inputs>
    <outputs>

        <collection name="output_mgf_collection" type="list" label="${tool.name} on ${on_string}: MGF collection">
            <filter>output_format == "0"</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mgf" directory="output_folder" ext="mgf"/>
        </collection>

        <collection name="output_mzml_collection" type="list" label="${tool.name} on ${on_string}: mzML collection">
            <filter>output_format == "1"</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mzML" ext="mzml" directory="output_folder"/>
        </collection>

        <collection name="output_indexedmzml_collection" type="list" label="${tool.name} on ${on_string}: Indexed mzML collection">
            <filter>output_format == "2"</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mzML" ext="mzml" directory="output_folder"/>
        </collection>

        <collection name="output_metadata_collection" type="list" label="${tool.name} on ${on_string}: metadata collection">
            <filter>output_metadata_selector != "off"</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)-metadata.txt" ext="txt" directory="output_folder"/>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)-metadata.json" ext="json" directory="output_folder"/>
        </collection>

    </outputs>

    <tests>
        <!-- Basic mgf test - 1 file -->
        <test expect_num_outputs="1">
            <param name="input_files" value="really_small.raw" ftype="thermo.raw"/>
            <param name="output_format" value="0"/>
            <output_collection name="output_mgf_collection" type="list" count="1"/>

            <!--<output name="output" file="really_small.mzml" ftype="mzml" compare="sim_size" delta="3000" />-->
        </test>


        <!-- Basic mzml test - 2 files -->
        <test expect_num_outputs="1">
            <param name="input_files" value="really_small.raw,really_small_2.raw" ftype="thermo.raw"/>
            <param name="output_format" value="1"/>
            <output_collection name="output_mzml_collection" type="list" count="2"/>
        </test>

        <!-- Testing contents of converted mgf file with txt metadata -->
        <test expect_num_outputs="2">
            <param name="input_files" value="really_small.raw" ftype="thermo.raw"/>
            <param name="output_format" value="0"/>
            <param name="output_metadata_selector" value="1"/>
            <output_collection name="output_mgf_collection" type="list" count="1">
                <element name="really_small" ftype="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>
                </element>
            </output_collection>
            <output_collection name="output_metadata_collection" type="list">
                <element name="really_small" 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, 0.500]"/>
                        <has_text text="Number of scans=101"/>
                        <has_text text="Scan range=1;101"/>
                        <has_text text="Scan start time=[MS, MS:1000016, scan start time, 0.89]"/>
                        <has_text text="Time range=0.89;1.59"/>
                        <has_text text="Mass range=120.0000;2000.0000"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>

        <!-- mgf collection test with metadata -->
        <test expect_num_outputs="2">
            <param name="input_files" value="really_small.raw,really_small_2.raw,really_small_3.raw"/>
            <param name="output_format" value="0"/>
            <param name="output_metadata_selector" value="0"/>
            <output_collection name="output_mgf_collection" type="list" count="3"/>
            <output_collection name="output_metadata_collection" type="list" count="3"/>
        </test>
    </tests>
    <help>
<![CDATA[

Thermo RAW file converter based on the great `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ project.

]]>
    </help>
    <citations>
        <citation type="bibtex">@misc{Galaxy Proteomics Tools,
        author = {Niels Hulstaert, et al.},
        title = {Galaxy Proteomics Tools},
        publisher = {GitHub},
        journal = {GitHub repository},
        year = {2017}, url = {https://github.com/compomics/ThermoRawFileParser}}
        </citation>
    </citations>
</tool>

9:92ac8e086317

<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@">1.3.2</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, 0.500]"/>
                    <has_text text="Number of scans=101"/>
                    <has_text text="Scan range=1;101"/>
                    <has_text text="Scan start time=[MS, MS:1000016, scan start time, 0.89]"/>
                    <has_text text="Time range=0.89;1.59"/>
                    <has_text text="Mass range=120.0000;2000.0000"/>
                </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=&quot;1&quot;"/>
            </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>