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1 <tool id ="pyGetGTFSources" name="pyGetGTFSources">
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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/pyGetGTFSources.py --gtf $addGTF.gtf --count -o $out
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7 </command>
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8 <version_command>/usr/local/bin/pyGetGTFSources.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="count" type="select" label="Count occurences of each annotation --count">
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25 <option value="" selected="true">No</option>
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26 <option value="--count">Yes</option>
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27 </param>
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28 <param name="label" type="text" format="txt" size="30" value="GTF sources list" label="Enter output file label -o" />
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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="out" label="${label.value}.txt"/>
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33 </outputs>
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34 <help>
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35 .. class:: infomark
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36
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37 **pyGetGTFSources**
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38
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39 pyGetGTFSources is part of the pyCRAC_ package. Extracts source names from the second column in a GTF file.
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40
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41
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42 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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43
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44 ------
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45
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46 **Parameter list**
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47
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48 Options::
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49
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50 --gtf=Yourfavoritegtf.gtf
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51 type the path to the gtf file that you want to use. By
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52 default it expects data from the standard input
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53 -o OUTFILE, --outfile=OUTFILE
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54 type the name and path of the file you want to write
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55 the output to. Default is standard output
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56 --count with this flag you the program will count the
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57 occurence for each source/annotation in the gtf file
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58
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59
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60
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61
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62 </help>
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63 </tool>
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