comparison abims_xcms_xcmsSet.xml @ 24:d8915395681f draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d

23:329cfa3d2be6

    <expand macro="stdio"/>

    <command><![CDATA[
        @COMMAND_XCMS_SCRIPT@

        #if $inputs.input == "zip_file":
            zipfile '$inputs.zip_file'
        #elif $inputs.input == "single_file":
            singlefile_galaxyPath '$inputs.single_file' singlefile_sampleName '$inputs.single_file.name'
        #end if

        xfunction xcmsSet

        xsetRdataOutput '$xsetRData'

        @COMMAND_LOG_EXIT@
    ]]></command>

    <inputs>

      <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">mzXML 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" />
            </when>
        </conditional>

        <conditional name="options_scanrange">
            <param name="option" type="select" label="Scan range option " >
                <option value="show">show</option>
                <option value="hide" selected="true">hide</option>

                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>-->
        <test>
            <param name="inputs|input" value="zip_file" />
            <param name="inputs|zip_file" value="faahKO_reduce.zip"  ftype="zip" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>-->
        <test>
            <param name="inputs|input" value="single_file" />
            <param name="inputs|single_file" value="HU_neg_017.mzXML"  ftype="mzxml" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="inputs|input" value="single_file" />
            <param name="inputs|single_file" value="MM14.mzML"  ftype="mzxml" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="56" />
            <param name="methods|peakwidth" value="5.275,13.5" />
            <output name="log">
                <assert_contents>

-----------
Input files
-----------

+---------------------------+--------------------+
| Parameter : num + label   |   Format           |
+===========================+====================+
| OR : Zip file             |   zip              |
+---------------------------+--------------------+
| OR : Single file          |   mzXML, netCDF    |
+---------------------------+--------------------+

**Choose your inputs**

You have two methods for your inputs:

    | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
    | Single file: You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"

Zip file: Steps for creating the zip file
-----------------------------------------

**Step1: Creating your directory and hierarchize the subdirectories**

24:d8915395681f

    <expand macro="stdio"/>

    <command><![CDATA[
        @COMMAND_XCMS_SCRIPT@

        #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
            singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
        #else
            zipfile '$input'
        #end if

        xfunction xcmsSet

        xsetRdataOutput '$xsetRData'

        @COMMAND_LOG_EXIT@
    ]]></command>

    <inputs>

        <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />

        <conditional name="options_scanrange">
            <param name="option" type="select" label="Scan range option " >
                <option value="show">show</option>
                <option value="hide" selected="true">hide</option>

                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>-->
        <test>
            <param name="input" value="faahKO_reduce.zip"  ftype="zip" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>-->
        <test>
            <param name="input" value="HU_neg_017.mzXML"  ftype="mzxml" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="MM14.mzML"  ftype="mzxml" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="56" />
            <param name="methods|peakwidth" value="5.275,13.5" />
            <output name="log">
                <assert_contents>

-----------
Input files
-----------

+---------------------------+----------------------------------+
| Parameter : num + label   |   Format                         |
+===========================+==================================+
| OR : Zip file             |   zip                            |
+---------------------------+----------------------------------+
| OR : Single file          |   mzXML, mzML, mzData, netCDF    |
+---------------------------+----------------------------------+

**Choose your inputs**

You have two methods for your inputs:

    | Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"
    | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).

Zip file: Steps for creating the zip file
-----------------------------------------

**Step1: Creating your directory and hierarchize the subdirectories**