view macros.xml @ 25:230f0bc9e792 draft

planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
	    <requirement type="package" version="0.4_1">r-snow</requirement>
            <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
            <requirement type="package" version="2.26.0">bioconductor-multtest</requirement>
	    <requirement type="package" version="1.1_4">r-batch</requirement>
            <requirement type="package" version="1.6.27">libpng</requirement>
            <requirement type="package" version="1.3.20">graphicsmagick</requirement>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1" level="fatal" />
        </stdio>
    </xml>

    <token name="@COMMAND_CAMERA_SCRIPT@">
        LANG=C Rscript $__tool_directory__/CAMERA.r
    </token>

    <!-- zipfile load for planemo test -->
    <token name="@COMMAND_FILE_LOAD@">
        #if $file_load_conditional.file_load_select == "yes":
            #if $file_load_conditional.inputs.input == "zip_file":
                zipfile '$file_load_conditional.inputs.zip_file'
            #else
                #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] )
                #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] )

                singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
            #end if
        #end if
    </token>

    <xml name="file_load">
        <conditional name="file_load_conditional">
            <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
                <option value="no" >no need</option>
                <option value="yes" >yes</option>
            </param>
            <when value="no">
            </when>
            <when value="yes">
                <conditional name="inputs">
                    <param name="input" type="select" label="Choose your inputs method" >
                        <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
                        <option value="single_file">A mzXML or netCDF file from your history</option>
                    </param>
                    <when value="zip_file">
                        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
                    </when>
                    <when value="single_file">
                        <param name="single_file" type="data" format="mzxml,netcdf" label="Single file"  multiple="true"/>
                    </when>
                </conditional>
            </when>
        </conditional>
    </xml>

    <token name="@COMMAND_PEAKLIST@">
        convertRTMinute $convertRTMinute
        numDigitsMZ $numDigitsMZ
        numDigitsRT $numDigitsRT
        intval $intval
    </token>

    <xml name="input_peaklist">
        <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="General used intensity value" 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>
    </xml>

    <token name="@HELP_AUTHORS@">
.. class:: infomark

**Authors**  Colin A. Smith [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann [e-mail], Paul Benton [e-mail] and Christopher Conley [e-mail]

.. class:: infomark

**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton [e-mail] - part of Workflow4Metabolomics.org [W4M]

 | Contact [e-mail] for any questions or concerns about the Galaxy implementation of this tool.

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

    </token>


    <xml name="citation">
        <citations>
            <citation type="doi">10.1021/ac202450g</citation>
            <citation type="doi">10.1093/bioinformatics/btu813</citation>
        </citations>
    </xml>
</macros>