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1 <tool id="abundance_estimation_to_matrix" name="abundance_estimation_to_matrix" version="0.0.1">
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2
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3 <description>Join RSEM estimates from multiple samples into a single matrix</description>
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4 <requirements>
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5 <requirement type="package">trinity</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8
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9 abundance_estimation_to_matrix_wrapper.py
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10 #for $q in $RSEM_samples
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11 ${q.file} "${q.column_label}"
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12 #end for
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13
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14 </command>
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15 <inputs>
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16
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17 <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
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18 <param name="file" label="Add file" type="data" format="text"/>
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19 <param name="column_label" label="column label" type="text" />
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20 </repeat>
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21
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22 </inputs>
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23 <outputs>
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24 <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/>
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25 </outputs>
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26 <tests>
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27
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28
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29 <test>
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30 <param name="target" value="trinity/Trinity.fasta" />
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31 <param name="aligner" value="bowtie" />
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32 <param name="paired_or_single" value="single" />
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33 <param name="library_type" value="None" />
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34 <param name="input" value="trinity/reads.left.fq" />
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35 </test>
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36
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37
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38 </tests>
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39 <help>
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40 .. _Trinity: http://trinityrnaseq.sourceforge.net
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41 </help>
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42 </tool>
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