comparison abims_xcms_fillPeaks.xml @ 11:de0d85537ee3 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797

10:6caa60dcc217

<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.8">

    <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description>

    <macros>
        <import>macros.xml</import>

    <expand macro="stdio"/>

    <command><![CDATA[
        @COMMAND_XCMS_SCRIPT@
        xfunction fillPeaks
        image $image

        xsetRdataOutput $xsetRData

        method $method

        #if $peaklist.peaklistBool
            variableMetadataOutput $variableMetadata
            dataMatrixOutput $dataMatrix
            convertRTMinute $peaklist.convertRTMinute
            numDigitsMZ $peaklist.numDigitsMZ
            numDigitsRT $peaklist.numDigitsRT
            intval $peaklist.intval
        #end if

        @COMMAND_ZIPFILE_LOAD@

        @COMMAND_LOG_EXIT@

    ]]></command>

        <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />
        <param name="method" type="select" label="Filling method" help="[method] See the help section below">
            <option value="chrom" selected="true">chrom</option>
            <option value="MSW" >MSW</option>
        </param>
        <conditional name="peaklist">
            <param name="peaklistBool" type="boolean" label="Get a Peak List" />
            <when value="true">
              <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
              <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
              <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
              <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
                  <option value="into" selected="true">into</option>
                  <option value="maxo">maxo</option>
                  <option value="intb">intb</option>
              </param>
            </when>
            <when value="false" />
        </conditional>
        <expand macro="zipfile_load"/>

    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv">
            <filter>(peaklist['peaklistBool'])</filter>
        </data>
        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" >
            <filter>(peaklist['peaklistBool'])</filter>
        </data>
        <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
    </outputs>

    <tests>
        <!--<test>

                <param name="convertRTMinute" value="false" />
                <param name="peaklistBool" value="true" />
                <param name="numDigitsMZ" value="4" />
                <param name="numDigitsRT" value="1" />
            </conditional>
            <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
            <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip"  ftype="zip" />
            <output name="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
                    <has_text text="Mass range: 200.1-600 m/z" />

---------------------------------------------------

Changelog/News
--------------

**Version 2.0.8 - 22/12/2016**

- IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate

**Version 2.0.7 - 06/07/2016**

**Version 2.0.6 - 04/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies


**Version 2.0.5 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- UPDATE: refactoring of internal management of inputs/outputs

11:de0d85537ee3

<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.0">

    <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description>

    <macros>
        <import>macros.xml</import>

    <expand macro="stdio"/>

    <command><![CDATA[
        @COMMAND_XCMS_SCRIPT@
        xfunction fillPeaks
        image '$image'

        xsetRdataOutput '$xsetRData'

        method $method

        @COMMAND_PEAKLIST@

        @COMMAND_FILE_LOAD@

        @COMMAND_LOG_EXIT@

    ]]></command>

        <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />
        <param name="method" type="select" label="Filling method" help="[method] See the help section below">
            <option value="chrom" selected="true">chrom</option>
            <option value="MSW" >MSW</option>
        </param>

        <expand macro="input_peaklist"/>

        <expand macro="input_file_load"/>

    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
        <expand macro="output_peaklist" function="fillpeaks" />
        <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
    </outputs>

    <tests>
        <!--<test>

                <param name="convertRTMinute" value="false" />
                <param name="peaklistBool" value="true" />
                <param name="numDigitsMZ" value="4" />
                <param name="numDigitsRT" value="1" />
            </conditional>
            <expand macro="test_file_load_zip"/>
            <output name="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
                    <has_text text="Mass range: 200.1-600 m/z" />
                    <has_text text="Peaks: 32720 (about 8180 per sample)" />
                    <has_text text="Peak Groups: 8157" />
                    <has_text text="Sample classes: KO, WT" />
                </assert_contents>
            </output>
            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
            <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
        </test>
        <test>
            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData"/>
            <param name="method" value="chrom"/>
            <conditional name="peaklist">
                <param name="convertRTMinute" value="false" />
                <param name="peaklistBool" value="true" />
                <param name="numDigitsMZ" value="4" />
                <param name="numDigitsRT" value="1" />
            </conditional>
            <expand macro="test_file_load_single"/>
            <output name="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
                    <has_text text="Mass range: 200.1-600 m/z" />

---------------------------------------------------

Changelog/News
--------------

**Version 2.1.0 - 07/02/2017**

- IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)

- IMPROVEMENT: xcms.fillpeaks can deal with merged individual data

**Version 2.0.8 - 22/12/2016**

- IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate

**Version 2.0.7 - 06/07/2016**

**Version 2.0.6 - 04/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies

**Version 2.0.5 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- UPDATE: refactoring of internal management of inputs/outputs