view macros.xml @ 3:f24b9c360a60 draft

planemo upload commit dc4b1363a3fe83f195167f1f0b25c9728006e364

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.4_1">r-snow</requirement>
            <requirement type="package" version="1.0">r-probmetab</requirement>
            <requirement type="package" version="1.1_4">r-batch</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__/probmetab.r
    </token>

    <token name="@COMMAND_LOG_EXIT@">
        ;
        return=\$?;
        mv log.txt '$log';
        cat '$log';
        sh -c "exit \$return"
    </token>

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

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

    <token name="@COMMAND_FILE_LOAD_ONE@">
        #set file_load_section_selected = $file_load_section
        #set polarity=""
        @COMMAND_FILE_LOAD_NEUTRAL@
    </token>

    <token name="@COMMAND_FILE_LOAD_POSITIVE@">
        #set file_load_section_selected = $file_load_sectionPositive
        #set polarity="Positive"
        @COMMAND_FILE_LOAD_NEUTRAL@
    </token>

    <token name="@COMMAND_FILE_LOAD_NEGATIVE@">
        #set file_load_section_selected = $file_load_sectionNegative
        #set polarity="Negative"
        @COMMAND_FILE_LOAD_NEUTRAL@
    </token>

    <xml name="input_file_load" token_polarity="">
        <section name="file_load_section@POLARITY@" title="@POLARITY@ Resubmit your raw dataset or your zip file">
            <conditional name="file_load_conditional">
                <param name="file_load_select" type="select" label="@POLARITY@ 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>
        </section>
    </xml>

    <xml name="test_file_load_zip">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <conditional name="inputs">
                    <param name="input" value="zip_file" />
                    <param name="zip_file" value="faahKO_reduce.zip"  ftype="zip" />
                </conditional>
            </conditional>
        </section>
    </xml>

    <xml name="test_file_load_single" token_polarity="">>
        <section name="file_load_section@POLARITY@">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <conditional name="inputs">
                    <param name="input" value="single_file" />
                    <param name="single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF"  ftype="netcdf" />
                </conditional>
            </conditional>
        </section>
    </xml>

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

**Authors** Ricardo R. Silva et al. (2013) [e-mail]

 | If you use this tool, please cite: Silva RR and al.(2010). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics..
 | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/

.. class:: infomark

**Galaxy integration** Misharl Monsoor [e-mail] ABIMS TEAM, Station biologique de Roscoff.

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

.. class:: infomark

**Contributors**  Ricardo R. Silva [e-mail], Yann Guitton [e-mail] and Jean-François Martin [e-mail]

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

    </token>


    <xml name="citation">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btu019</citation>
            <citation type="doi">10.1093/bioinformatics/btu813</citation>
        </citations>
    </xml>
</macros>