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comparison SMART/galaxy/restrictTranscriptList.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
1 <tool id="restrictTranscriptList" name="restrict transcript list">
2 <description>Select the features which are located in a given locus.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> ../Java/Python/restrictTranscriptList.py -i $formatType.inputFileName
7 #if $formatType.FormatInputFileName == 'bed':
8 -f bed
9 #elif $formatType.FormatInputFileName == 'gff':
10 -f gff
11 #elif $formatType.FormatInputFileName == 'gff2':
12 -f gff2
13 #elif $formatType.FormatInputFileName == 'gff3':
14 -f gff3
15 #elif $formatType.FormatInputFileName == 'sam':
16 -f sam
17 #elif $formatType.FormatInputFileName == 'gtf':
18 -f gtf
19 #end if
20
21 #if $OptionChrom.Chrom == "Yes":
22 -c $OptionChrom.ChromName
23 #end if
24
25 #if $OptionStart.start == "Yes":
26 -s $OptionStart.startValue
27 #end if
28
29 #if $OptionEnd.end == "Yes":
30 -e $OptionEnd.endValue
31 #end if
32
33 -o $outputFile
34
35 </command>
36
37
38 <inputs>
39 <conditional name="formatType">
40 <param name="FormatInputFileName" type="select" label="Input File Format">
41 <option value="bed">bed</option>
42 <option value="gff">gff</option>
43 <option value="gff2">gff2</option>
44 <option value="gff3">gff3</option>
45 <option value="sam">sam</option>
46 <option value="gtf">gtf</option>
47 </param>
48 <when value="bed">
49 <param name="inputFileName" format="bed" type="data" label="Input File"/>
50 </when>
51 <when value="gff">
52 <param name="inputFileName" format="gff" type="data" label="Input File"/>
53 </when>
54 <when value="gff2">
55 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
56 </when>
57 <when value="gff3">
58 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
59 </when>
60 <when value="sam">
61 <param name="inputFileName" format="sam" type="data" label="Input File"/>
62 </when>
63 <when value="gtf">
64 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
65 </when>
66 </conditional>
67
68 <conditional name="OptionChrom">
69 <param name="Chrom" type="select" label="chromosome name">
70 <option value="Yes">Yes</option>
71 <option value="No" selected="true">No</option>
72 </param>
73 <when value="Yes">
74 <param name="ChromName" type="text" value="None"/>
75 </when>
76 <when value="No">
77 </when>
78 </conditional>
79
80 <conditional name="OptionStart">
81 <param name="start" type="select" label="start region of the locus">
82 <option value="Yes">Yes</option>
83 <option value="No" selected="true">No</option>
84 </param>
85 <when value="Yes">
86 <param name="startValue" type="integer" value="0"/>
87 </when>
88 <when value="No">
89 </when>
90 </conditional>
91
92 <conditional name="OptionEnd">
93 <param name="end" type="select" label="end region of the locus">
94 <option value="Yes">Yes</option>
95 <option value="No" selected="true">No</option>
96 </param>
97 <when value="Yes">
98 <param name="endValue" type="integer" value="0"/>
99 </when>
100 <when value="No">
101 </when>
102 </conditional>
103 </inputs>
104
105 <outputs>
106 <data format="gff3" name="outputFile" label="[restrict transcript list] output file"/>
107 </outputs>
108
109 <help>
110 Reads a list of genomic coordinates and outputs those which on a given chromosome and / or between two given positions.
111 </help>
112 <tests>
113 <test>
114 <param name="FormatInputFileName" value="gtf" />
115 <param name="inputFileName" value="genes.gtf" />
116 <param name="Chrom" value="Yes"/>
117 <param name="ChromName" value="I"/>
118 <param name="start" value="No" />
119 <param name="end" value="No" />
120 <output name="outputFile" file="exp_restrictTranscriptList.gff3" />
121 </test>
122 </tests>
123
124 </tool>