Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/restrictTranscriptList.xml @ 31:0ab839023fe4

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
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30:5677346472b5 31:0ab839023fe4
1 <tool id="restrictTranscriptList" name="restrict transcript list"> 1 <tool id="restrictTranscriptList" name="restrict transcript list">
2 <description>Select the features which are located in a given locus.</description> 2 <description>Keep the coordinates which are located in a given position.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> ../Java/Python/restrictTranscriptList.py -i $formatType.inputFileName 3 <command interpreter="python"> ../Java/Python/restrictTranscriptList.py -i $formatType.inputFileName
7 #if $formatType.FormatInputFileName == 'bed': 4 #if $formatType.FormatInputFileName == 'bed':
8 -f bed 5 -f bed
9 #elif $formatType.FormatInputFileName == 'gff': 6 #elif $formatType.FormatInputFileName == 'gff':
10 -f gff 7 -f gff
76 <when value="No"> 73 <when value="No">
77 </when> 74 </when>
78 </conditional> 75 </conditional>
79 76
80 <conditional name="OptionStart"> 77 <conditional name="OptionStart">
81 <param name="start" type="select" label="start region of the locus"> 78 <param name="start" type="select" label="restrict to the start of the transcript">
82 <option value="Yes">Yes</option> 79 <option value="Yes">Yes</option>
83 <option value="No" selected="true">No</option> 80 <option value="No" selected="true">No</option>
84 </param> 81 </param>
85 <when value="Yes"> 82 <when value="Yes">
86 <param name="startValue" type="integer" value="0"/> 83 <param name="startValue" type="integer" value="0"/>
88 <when value="No"> 85 <when value="No">
89 </when> 86 </when>
90 </conditional> 87 </conditional>
91 88
92 <conditional name="OptionEnd"> 89 <conditional name="OptionEnd">
93 <param name="end" type="select" label="end region of the locus"> 90 <param name="end" type="select" label="restrict to the end of the transcript">
94 <option value="Yes">Yes</option> 91 <option value="Yes">Yes</option>
95 <option value="No" selected="true">No</option> 92 <option value="No" selected="true">No</option>
96 </param> 93 </param>
97 <when value="Yes"> 94 <when value="Yes">
98 <param name="endValue" type="integer" value="0"/> 95 <param name="endValue" type="integer" value="0"/>
101 </when> 98 </when>
102 </conditional> 99 </conditional>
103 </inputs> 100 </inputs>
104 101
105 <outputs> 102 <outputs>
106 <data format="gff3" name="outputFile" label="[restrict transcript list] output file"/> 103 <data format="gff3" name="outputFile" label="[restrictTranscriptList] Output File"/>
107 </outputs> 104 </outputs>
108 105
109 <help> 106 <help>
110 Reads a list of genomic coordinates and outputs those which on a given chromosome and / or between two given positions.
111 </help> 107 </help>
112 <tests> 108 <tests>
113 <test> 109 <test>
114 <param name="FormatInputFileName" value="gtf" /> 110 <param name="FormatInputFileName" value="gtf" />
115 <param name="inputFileName" value="genes.gtf" /> 111 <param name="inputFileName" value="genes.gtf" />