view plotheatmap.xml @ 0:c5a812cdf478 draft

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<tool id="plotheatmap" name="plotheatmap" version="1.0">
    <description>Make a count matrix for edgeR</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
        <![CDATA[ 
            $__tool_directory__/tools/script.R $count_matrix $stats_matrix $log_fc $log_cpm $pvalue $fdr > $rscript_log 2> $rerror_log



        ]]>
    </command>
    <inputs>
        <param name="count_matrix" type="data" format="data" label=""/>
        <param name="stats_matrix" type="data" format="data" label=""/>
        <param name="log_fc" type="float" value="0.5" label=""/>
        <param name="log_cpm" type="float" value="0.5" label=""/>
        <param name="pvalue" type="float" value="0.5" label=""/>
        <param name="fdr" type="float" value="0.5" label=""/>

    </inputs>
    <outputs>
<!--        <data name="output" format="data" /> --> 
       <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" >
            <filter>(outftype == 'pdf')</filter>
        </data>
        <data name="rscript_log" format="data" />
        <data name="rerror_log" format="data" />
    </outputs>
    <tests>

        <test>
            <param name="count_matrix" value="count.matrix"/>
            <param name="stats_matrix" value="stats.data"/>
            <param name="log_fc" value="1"/>
            <param name="log_cpm" value="2"/>
            <param name="pvalue" value="0.05"/>
            <param name="fdr" value="0.1"/>
<!--             <output name="output" file="done"/> -->
            <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size" />
            <output name="rscript_log" file="rscript.log"/>
            <output name="rerror_log" file="rerror.log"/>

        </test>

    </tests>
    <help>
        <![CDATA[ 

tutaj cos bedzie
     ]]>
    </help>
    <citations>
        
    </citations>
</tool>