Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/restrictTranscriptList.xml @ 15:440ceca58672
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| author | m-zytnicki |
|---|---|
| date | Mon, 22 Apr 2013 11:08:07 -0400 |
| parents | 769e306b7933 |
| children | 94ab73e8a190 |
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| 14:c79b9ae3f65f | 15:440ceca58672 |
|---|---|
| 1 <tool id="restrictTranscriptList" name="restrict transcript list"> | 1 <tool id="restrictTranscriptList" name="restrict transcript list"> |
| 2 <description>Keep the coordinates which are located in a given position.</description> | 2 <description>Select the features which are located in a given locus.</description> |
| 3 <command interpreter="python"> ../Java/Python/restrictTranscriptList.py -i $formatType.inputFileName | 3 <command interpreter="python"> ../Java/Python/restrictTranscriptList.py -i $formatType.inputFileName |
| 4 #if $formatType.FormatInputFileName == 'bed': | 4 #if $formatType.FormatInputFileName == 'bed': |
| 5 -f bed | 5 -f bed |
| 6 #elif $formatType.FormatInputFileName == 'gff': | 6 #elif $formatType.FormatInputFileName == 'gff': |
| 7 -f gff | 7 -f gff |
| 73 <when value="No"> | 73 <when value="No"> |
| 74 </when> | 74 </when> |
| 75 </conditional> | 75 </conditional> |
| 76 | 76 |
| 77 <conditional name="OptionStart"> | 77 <conditional name="OptionStart"> |
| 78 <param name="start" type="select" label="restrict to the start of the transcript"> | 78 <param name="start" type="select" label="start region of the locus"> |
| 79 <option value="Yes">Yes</option> | 79 <option value="Yes">Yes</option> |
| 80 <option value="No" selected="true">No</option> | 80 <option value="No" selected="true">No</option> |
| 81 </param> | 81 </param> |
| 82 <when value="Yes"> | 82 <when value="Yes"> |
| 83 <param name="startValue" type="integer" value="0"/> | 83 <param name="startValue" type="integer" value="0"/> |
| 85 <when value="No"> | 85 <when value="No"> |
| 86 </when> | 86 </when> |
| 87 </conditional> | 87 </conditional> |
| 88 | 88 |
| 89 <conditional name="OptionEnd"> | 89 <conditional name="OptionEnd"> |
| 90 <param name="end" type="select" label="restrict to the end of the transcript"> | 90 <param name="end" type="select" label="end region of the locus"> |
| 91 <option value="Yes">Yes</option> | 91 <option value="Yes">Yes</option> |
| 92 <option value="No" selected="true">No</option> | 92 <option value="No" selected="true">No</option> |
| 93 </param> | 93 </param> |
| 94 <when value="Yes"> | 94 <when value="Yes"> |
| 95 <param name="endValue" type="integer" value="0"/> | 95 <param name="endValue" type="integer" value="0"/> |
| 103 <data format="gff3" name="outputFile" label="[restrictTranscriptList] Output File"/> | 103 <data format="gff3" name="outputFile" label="[restrictTranscriptList] Output File"/> |
| 104 </outputs> | 104 </outputs> |
| 105 | 105 |
| 106 <help> | 106 <help> |
| 107 </help> | 107 </help> |
| 108 <tests> | |
| 109 <test> | |
| 110 <param name="FormatInputFileName" value="gtf" /> | |
| 111 <param name="inputFileName" value="genes.gtf" /> | |
| 112 <param name="Chrom" value="Yes"/> | |
| 113 <param name="ChromName" value="I"/> | |
| 114 <param name="start" value="No" /> | |
| 115 <param name="end" value="No" /> | |
| 116 <output name="outputFile" file="exp_restrictTranscriptList.gff3" /> | |
| 117 </test> | |
| 118 </tests> | |
| 119 | |
| 120 <help> | |
| 121 Reads a list of genomic coordinates and outputs those which on a given chromosome and / or between two given positions. | |
| 122 </help> | |
| 123 | |
| 108 </tool> | 124 </tool> |