comparison macros.xml @ 3:f24b9c360a60 draft

planemo upload commit dc4b1363a3fe83f195167f1f0b25c9728006e364

2:9541ba588de1

    </xml>

    <token name="@COMMAND_CAMERA_SCRIPT@">
        LANG=C Rscript $__tool_directory__/probmetab.r
    </token>
    
    <!-- zipfile load for planemo test -->
    <token name="@COMMAND_ZIPFILE_LOAD@">
        #if $zipfile_load_conditional.zipfile_load_select == "yes":
            #if $zipfile_load_conditional.zip_file:
                zipfile $zipfile_load_conditional.zip_file
            #end if
        #end if    
    </token>
    <xml name="zipfile_load">
        <conditional name="zipfile_load_conditional">
            <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." >
                <option value="no" >no need</option>
                <option value="yes" selected="peakgroups">yes</option>
            </param>
            <when value="no">
            </when>
            <when value="yes">
                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
            </when>
        </conditional>
    </xml>
    
    <token name="@HELP_AUTHORS@">
.. class:: infomark

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

3:f24b9c360a60

    </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]