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1 <tool id="preEBSeq" name="Preprocess files for EBSeq" version="0.1.0">
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2 <description>Generate expression matrix and IGvector file for EBSeq</description>
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3 <command interpreter="python">
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4 pre_EBSeq.py
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5 --outtable=$outtable
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6 --outvector=$outvector
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7 #for $i, $input in enumerate ( $batch_condition.levels ):
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8 #for $j, $input_rep in enumerate ($input.rep_counts ):
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9 --inputs "${input_rep.count_data}" "${input_rep.label}"
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10 #end for
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11 #end for
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12
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13 </command>
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14 <inputs>
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15 <repeat name="rep_counts" title="Raw counts" min="2">
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16 <param name="count_data" type="data" format="txt" label="Raw count"/>
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17 <param name="label" format="txt" type="text" value="file1" label="File label name" help="You need to specify an unique label name for your replicates.">
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18 <sanitizer>
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19 <valid initial="string.letters,string.digits">
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20 <add value="_" />
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21 </valid>
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22 <mapping initial="none">
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23 <add source=" " target="_"/>
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24 </mapping>
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25 </sanitizer>
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26 </param>
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27 </repeat>
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28
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29 </inputs>
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30
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31 <outputs>
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32 <data format="tabular" name="outtable" label="Expression matrix (on ${on_string})" />
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33 <data format="tabular" name="outvector" label="IGvector file (on ${on_string})"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37
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38 </test>
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39 </tests>
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40 <help>
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41 -----------
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42 Description
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43 -----------
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44 Build Expression Table and IGvector fles from RSEM output to EBSeq input
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45
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46 </help>
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47 </tool> |
