comparison abims_xcms_fillPeaks.xml @ 4:2edfa5e1f719 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6

3:5a54397dbc97

<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.5">

    <description>Integrate the signal in the region of that peak group not represented and create a new peak</description>

    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="1.44.0">xcms</requirement>
        <requirement type="package" version="2.2.0">xcms_w4m_script</requirement>
    </requirements>
    
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

    <command><![CDATA[
        xcms.r 
        xfunction fillPeaks 
        image $image 

        xsetRdataOutput $xsetRData

        method $method

        ###if $zip_file:
        ##    zipfile $zip_file
        ###end if
        ;
        return=\$?;
        mv log.txt $log;
        cat $log;
        sh -c "exit \$return"
        
    ]]></command>

    <inputs>
        <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (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>
        <!-- To pass planemo test -->
        <!--<param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />-->
    </inputs>

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

    
    <tests>
        <test>
            <param name="image" value="xset.group.retcor.group.RData"/>
            <param name="method" value="chrom"/>
            <param name="zip_file" value="sacuri.zip"/>
            <!--<output name="xsetRData" file="xset.group.retcor.group.fillPeaks.RData" />-->
            <output name="log">
                <assert_contents>
                    <has_text text="object with 9 samples" />
                    <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" />
                    <has_text text="Mass range: 50.0019-999.9863 m/z" />
                    <has_text text="Peaks: 157780 (about 17531 per sample)" />
                    <has_text text="Peak Groups: 6761" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[

        
.. 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.


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

==============
Xcms.fillPeaks
==============

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

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

**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

- IMPROVEMENT: parameter labels have changed to facilitate their reading.


    ]]></help>

    <citations>
        <citation type="doi">10.1021/ac051437y</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </citations>


</tool>

4:2edfa5e1f719

<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.6">

    <description>Integrate the signal in the region of that peak group not represented and create a new peak</description>

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

    <expand macro="requirements"/>
    <expand macro="stdio"/>

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

        xsetRdataOutput $xsetRData

        method $method

        #if $zip_file:
            zipfile $zip_file
        #end if
        @COMMAND_LOG_EXIT@ 
        
    ]]></command>

    <inputs>
        <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (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>
        <!-- To pass planemo test -->
        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." />
    </inputs>

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

    
    <tests>
        <test>
            <param name="image" value="xset.group.retcor.group.RData"/>
            <param name="method" value="chrom"/>
            <param name="zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
            <output name="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
                    <has_text text="Mass range: 50.0021-999.9863 m/z" />
                    <has_text text="Peaks: 199718 (about 49930 per sample)" />
                    <has_text text="Peak Groups: 48958" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
        
@HELP_AUTHORS@

==============
Xcms.fillPeaks
==============

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

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

**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

- IMPROVEMENT: parameter labels have changed to facilitate their reading.


    ]]></help>


    <expand macro="citation" />


</tool>