annotate macros.xml @ 11:fc1fa0c70378 draft

planemo upload commit f8a14a5bfd1843dc3f65b3f713c35dd62bf6996a-dirty

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.1.2">R</requirement>
	    <requirement type="package" version="0.4_1">r-snow</requirement>
            <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
            <requirement type="package" version="2.26.0">bioconductor-multtest</requirement>
	    <requirement type="package" version="1.1_4">r-batch</requirement>
            <requirement type="package" version="1.6.17">libpng</requirement>
            <requirement type="package" version="1.3.20">graphicsmagick</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__/CAMERA.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**  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.

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

    </token>


    <xml name="citation">
        <citations>
            <citation type="doi">10.1021/ac202450g</citation>
            <citation type="doi">10.1093/bioinformatics/btu813</citation>
        </citations>
    </xml>
</macros>