annotate trinityrnaseq_protocol/RSEM_estimates_to_matrix.xml @ 3:87c03e2aeba3 draft default tip

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<tool id="RSEM_estimates_to_matrix" name="RSEM_estimates_to_matrix" version="0.0.1">

    <description>Join RSEM estimates from multiple samples into a single matrix</description>
    <requirements>
        <requirement type="package">trinity</requirement>
    </requirements>
    <command interpreter="python">

        trinityToolWrapper.py util/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl

		--labels
        #for $entry in $RSEM_samples:
        	${entry.column_label}
        #end for

		--RSEM_counts
        #for $entry in $RSEM_samples:
        	${entry.file}
        #end for

        > RSEM.counts.matrix

    </command>
    <inputs>

       <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
              <param name="file" label="Add file" type="data" format="text"/>
              <param name="column_label" label="column label" type="text" />
       </repeat>

    </inputs>
    <outputs>
        <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.counts.matrix"/>
	</outputs>
    <tests>


		<test>
			<param name="target" value="trinity/Trinity.fasta" />
			<param name="aligner" value="bowtie" />
			<param name="paired_or_single" value="single" />
			<param name="library_type" value="None" />
			<param name="input" value="trinity/reads.left.fq" />
        </test>
	

    </tests>
    <help>
        .. _Trinity: http://trinityrnaseq.sourceforge.net
    </help>
</tool>