Mercurial > repos > yufei-luo > s_mart

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:e0f8dcca02ed
1 <tool id="plotGenomeCoverage" name="plot genome coverage">
2 <description>Get the coverage of a genome. </description>
3 <command interpreter="python"> ../Java/Python/plotGenomeCoverage.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 -r $reference
19 -o $outputFile
20 </command>
21
22
23 <inputs>
24 <conditional name="formatType">
25 <param name="FormatInputFileName" type="select" label="Input File Format">
26 <option value="bed">bed</option>
27 <option value="gff">gff</option>
28 <option value="gff2">gff2</option>
29 <option value="gff3">gff3</option>
30 <option value="sam">sam</option>
31 <option value="gtf">gtf</option>
32 </param>
33 <when value="bed">
34 <param name="inputFileName" format="bed" type="data" label="Input File"/>
35 </when>
36 <when value="gff">
37 <param name="inputFileName" format="gff" type="data" label="Input File"/>
38 </when>
39 <when value="gff2">
40 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
41 </when>
42 <when value="gff3">
43 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
44 </when>
45 <when value="sam">
46 <param name="inputFileName" format="sam" type="data" label="Input File"/>
47 </when>
48 <when value="gtf">
49 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
50 </when>
51 </conditional>
52
53 <param name="reference" type="data" label="reference Fasta File" format="fasta"/>
54 </inputs>
55
56 <outputs>
57 <data format="png" name="outputFile" label="[plotGenomeCoverage] Output File"/>
58 </outputs>
59
60 <help>
61 </help>
62 </tool>