Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/restrictTranscriptList.xml @ 15:440ceca58672

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Uploaded
author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
comparison
equal deleted inserted replaced
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>