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comparison smart_toolShed/SMART/galaxy/restrictTranscriptList.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 <tool id="restrictTranscriptList" name="restrict transcript list">
2 <description>Keep the coordinates which are located in a given position.</description>
3 <command interpreter="python"> ../Java/Python/restrictTranscriptList.py -i $formatType.inputFileName
4 #if $formatType.FormatInputFileName == 'bed':
5 -f bed
6 #elif $formatType.FormatInputFileName == 'gff':
7 -f gff
8 #elif $formatType.FormatInputFileName == 'gff2':
9 -f gff2
10 #elif $formatType.FormatInputFileName == 'gff3':
11 -f gff3
12 #elif $formatType.FormatInputFileName == 'sam':
13 -f sam
14 #elif $formatType.FormatInputFileName == 'gtf':
15 -f gtf
16 #end if
17
18 #if $OptionChrom.Chrom == "Yes":
19 -c $OptionChrom.ChromName
20 #end if
21
22 #if $OptionStart.start == "Yes":
23 -s $OptionStart.startValue
24 #end if
25
26 #if $OptionEnd.end == "Yes":
27 -e $OptionEnd.endValue
28 #end if
29
30 -o $outputFile
31
32 </command>
33
34
35 <inputs>
36 <conditional name="formatType">
37 <param name="FormatInputFileName" type="select" label="Input File Format">
38 <option value="bed">bed</option>
39 <option value="gff">gff</option>
40 <option value="gff2">gff2</option>
41 <option value="gff3">gff3</option>
42 <option value="sam">sam</option>
43 <option value="gtf">gtf</option>
44 </param>
45 <when value="bed">
46 <param name="inputFileName" format="bed" type="data" label="Input File"/>
47 </when>
48 <when value="gff">
49 <param name="inputFileName" format="gff" type="data" label="Input File"/>
50 </when>
51 <when value="gff2">
52 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
53 </when>
54 <when value="gff3">
55 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
56 </when>
57 <when value="sam">
58 <param name="inputFileName" format="sam" type="data" label="Input File"/>
59 </when>
60 <when value="gtf">
61 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
62 </when>
63 </conditional>
64
65 <conditional name="OptionChrom">
66 <param name="Chrom" type="select" label="chromosome name">
67 <option value="Yes">Yes</option>
68 <option value="No" selected="true">No</option>
69 </param>
70 <when value="Yes">
71 <param name="ChromName" type="text" value="None"/>
72 </when>
73 <when value="No">
74 </when>
75 </conditional>
76
77 <conditional name="OptionStart">
78 <param name="start" type="select" label="restrict to the start of the transcript">
79 <option value="Yes">Yes</option>
80 <option value="No" selected="true">No</option>
81 </param>
82 <when value="Yes">
83 <param name="startValue" type="integer" value="0"/>
84 </when>
85 <when value="No">
86 </when>
87 </conditional>
88
89 <conditional name="OptionEnd">
90 <param name="end" type="select" label="restrict to the end of the transcript">
91 <option value="Yes">Yes</option>
92 <option value="No" selected="true">No</option>
93 </param>
94 <when value="Yes">
95 <param name="endValue" type="integer" value="0"/>
96 </when>
97 <when value="No">
98 </when>
99 </conditional>
100 </inputs>
101
102 <outputs>
103 <data format="gff3" name="outputFile" label="[restrictTranscriptList] Output File"/>
104 </outputs>
105
106 <help>
107 </help>
108 </tool>