comparison abims_xcms_group.xml @ 4:2db1d1d0f131 draft

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

3:98e33cdf0eb1

<tool id="abims_xcms_group" name="xcms.group" version="2.0.4">

    <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</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 group 
        image $image 

        xsetRdataOutput $xsetRData
        rplotspdf $rplotsPdf

            mzVsRTbalance $methods.mzVsRTbalance
            mzCheck $methods.mzCheck
            rtCheck $methods.rtCheck
            kNN $methods.kNN
        #end if
        ;
        return=\$?;
        mv log.txt $log;
        cat $log;
        sh -c "exit \$return"
        
   ]]></command> 

    <inputs>
        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
        <conditional name="methods">

    </outputs>

    <tests>
        <test>
            <param name="image" value="xset.RData"/>
            <param name="methods.method" value="density"/>
            <param name="methods.bw" value="5"/>
            <param name="methods.minfrac" value="0.3"/>
            <param name="methods.mzwid" value="0.01"/>
            <param name="methods.density_options.option" value="show"/>
            <param name="methods.density_options.max" value="50"/>
            <!--<output name="xsetRData" file="xset.group.RData" />-->
            <!--<output name="rplotsPdf" file="xset.group.Rplots.pdf" />-->
            <output name="log">
                <assert_contents>
                    <has_text text="object with 9 samples" />
                    <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" />
                    <has_text text="Mass range: 50.0019-999.9863 m/z" />
                    <has_text text="Peaks: 135846 (about 15094 per sample)" />
                    <has_text text="Peak Groups: 6642" />
                    <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] 

**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.Group
==========

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

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

**Version 2.0.4 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- UPDATE: refactoring of internal management of inputs/outputs

    ]]></help>


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


</tool>

4:2db1d1d0f131

<tool id="abims_xcms_group" name="xcms.group" version="2.0.5">

    <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>

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

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

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

        xsetRdataOutput $xsetRData
        rplotspdf $rplotsPdf

            mzVsRTbalance $methods.mzVsRTbalance
            mzCheck $methods.mzCheck
            rtCheck $methods.rtCheck
            kNN $methods.kNN
        #end if
        @COMMAND_LOG_EXIT@
   ]]></command> 

    <inputs>
        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
        <conditional name="methods">

    </outputs>

    <tests>
        <test>
            <param name="image" value="xset.RData"/>
            <param name="methods|method" value="density"/>
            <param name="methods|bw" value="5"/>
            <param name="methods|minfrac" value="0.3"/>
            <param name="methods|mzwid" value="0.01"/>
            <param name="methods|density_options|option" value="show"/>
            <param name="methods|density_options|max" value="50"/>
            <output name="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
                    <has_text text="Mass range: 50.0021-999.9863 m/z" />
                    <has_text text="Peaks: 59359 (about 14840 per sample)" />
                    <has_text text="Peak Groups: 48998" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="image" value="xset.group.retcor.RData"/>
            <param name="methods|method" value="density"/>
            <param name="methods|bw" value="5"/>
            <param name="methods|minfrac" value="0.3"/>
            <param name="methods|mzwid" value="0.01"/>
            <param name="methods|density_options|option" value="show"/>
            <param name="methods|density_options|max" value="50"/>
            <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: 59359 (about 14840 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.Group
==========

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

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

**Version 2.0.5 - 04/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies 


**Version 2.0.4 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- UPDATE: refactoring of internal management of inputs/outputs

    ]]></help>


    <expand macro="citation" />


</tool>