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1 <tool id ="pyCheckGTFfile" name="pyCheckGTFfile">
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2 <requirements>
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3 <requirement type="package">pyCRAC</requirement>
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4 </requirements>
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5 <command interpreter="python">
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6 /usr/local/bin/pyCheckGTFfile.py --gtf $addGTF.gtf -o $out
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7 </command>
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8 <version_command>/usr/local/bin/pyCheckGTFfile.py --version</version_command>
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9 <inputs>
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10 <conditional name="addGTF">
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11 <param name="gtfFile" type="select" label="Choose GTF File from">
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12 <option value="default" selected="true">Defaults</option>
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13 <option value="other">History</option>
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14 </param>
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15 <when value="default">
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16 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
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17 <options from_data_table="pycrac_gtf"/>
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18 </param>
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19 </when>
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20 <when value="other">
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21 <param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
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22 </when>
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23 </conditional>
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24 <param name="label" type="text" format="txt" size="30" value="pyCheckGTFfile" label="Enter output file label -o" />
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25 </inputs>
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26
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27 <outputs>
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28 <data format="gtf" name="out" label="${label.value}.gtf"/>
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29 </outputs>
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30 <help>
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31 .. class:: infomark
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32
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33 **pyCheckGTFfile**
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34
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35 pyCheckGTFfile is part of the pyCRAC_ package. Renames duplicated gene names in your GTF annotation file.
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36
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37 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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38
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39 ------
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40
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41 **Parameter list**
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42
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43 Options::
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44
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45 --gtf=gtf input file
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46 type the path to the gtf file that you want to use.
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47 -o FILE, --output=FILE
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48 Optional. Specify the name of the output file. Default
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49 is standard output. Make sure it has the .gtf
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50 extension!
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51
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52 </help>
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53 </tool>
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