Mercurial > repos > morinlab > calc_cnsegments
annotate calc_cnsegements_titan.xml @ 0:c6e48c6ac606 draft default tip
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
| author | morinlab |
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| date | Tue, 11 Oct 2016 14:16:32 -0400 |
| parents | |
| children |
| rev | line source |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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1 <tool id="calc_cnsegments" name="calc_cnsegements" version="0.0.1"> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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2 <description> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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3 Calculate Copy Number Segments from TITAN output |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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4 </description> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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5 <command> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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6 <![CDATA[ |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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7 perl $__tool_directory__/calc_cnsegements_titan.pl |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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8 |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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9 #if $sampleid_source.sampleid_selector == "bamfile": |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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10 -id \$(basename $sampleid_source.sample_id | sed 's/.bam$//g' ) |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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11 #else: |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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12 -id $sampleid_source.sample_id |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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13 #end if |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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14 |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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15 -o $outfile |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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16 -s $symmetric |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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17 -igv $outIGV |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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18 -i $infile |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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19 |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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20 ]]> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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21 </command> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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22 <inputs> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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23 <conditional name="sampleid_source"> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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24 <param label="Choose the source to open the Sample Id" name="sampleid_selector" type="select"> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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25 <option value="bamfile">Bam File Name</option> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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26 <option value="manual">Manual</option> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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27 </param> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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28 <when value="bamfile"> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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29 <param type="data" format="bam" name="sample_id" label="Sequence Alignment File"/> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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30 </when> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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31 <when value="manual"> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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32 <param name="sample_id" type="text" label="Sample ID (Name)"/> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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33 </when> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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34 </conditional> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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35 <param type="data" format="txt" name="infile" label="SNP Summary Information (TITAN Output)"/> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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36 <param type="boolean" name="symmetric" label="Symmetric" checked="yes" truevalue="1" falsevalue="0"/> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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37 </inputs> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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38 <outputs> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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39 <data format="txt" name="outfile"/> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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40 <data format="seg" name="outIGV"/> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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41 </outputs> |
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c6e48c6ac606
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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42 </tool> |