comparison samples_qccheck.xml @ 8:258c64019e50 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 811337eaab815f54f0fd93a3dd23a1153993ea2a

7:1b7800489efb

    </requirements>
    <stdio>
        <exit_code range="1:"/>
    </stdio>
    <command><![CDATA[
        
        ln -s "${matrix}" "input.matrix"
        
        &&
        
        PtR
        --matrix "input.matrix"
        
        --samples "${samples}"
        
        --CPM --log2 --compare_replicates
        
        &&
        
        PtR
        --matrix "input.matrix"
        
        --samples "${samples}"
        
        --CPM --log2 --sample_cor_matrix
        
        &&
        
        PtR
        --matrix "input.matrix"
        
        --samples "${samples}"
        
        --CPM --log2 --prin_comp 3
        
        && mkdir out_pdf
        && mv *rep_compare.pdf out_pdf/
        && mv *sample_cor_matrix.pdf out_pdf/
        && mv *principal_components.pdf out_pdf/
        
    ]]></command>
    <inputs>
        <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
        <param format="tabular" name="samples" type="data" label="Samples description" help="file describing samples and replicates"/>
    </inputs>
    <outputs>
        <collection name="reports" type="list" label="Quality check result files on ${on_string}">
            <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" visible="true" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>

.. _Trinity: http://trinityrnaseq.github.io
]]>
    </help>
    
     <citations>
        <citation type="doi">10.1038/nbt.1883</citation>
    </citations>
</tool>

8:258c64019e50

    </requirements>
    <stdio>
        <exit_code range="1:"/>
    </stdio>
    <command><![CDATA[

        ln -s "${matrix}" "input.matrix"

        &&

        PtR
        --matrix "input.matrix"

        --samples "${samples}"

        --CPM --log2 --compare_replicates

        &&

        PtR
        --matrix "input.matrix"

        --samples "${samples}"

        --CPM --log2 --sample_cor_matrix

        &&

        PtR
        --matrix "input.matrix"

        --samples "${samples}"

        --CPM --log2 --prin_comp 3

        && mkdir out_pdf
        && mv *rep_compare.pdf out_pdf/
        && mv *sample_cor_matrix.pdf out_pdf/
        && mv *principal_components.pdf out_pdf/

    ]]></command>
    <inputs>
        <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
        <param format="tabular" name="samples" type="data" label="Samples description" help="file describing samples and replicates"/>
    </inputs>
    <outputs>
        <collection name="reports" type="list" label="Quality check result files on ${on_string}">
            <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>

.. _Trinity: http://trinityrnaseq.github.io
]]>
    </help>

     <citations>
        <citation type="doi">10.1038/nbt.1883</citation>
    </citations>
</tool>