Mercurial > repos > yufei-luo > s_mart

annotate SMART/galaxy/plotGenomeCoverage.xml @ 11:2da30502c2f1

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated CompareOverlappingSmallQuery.xml
author m-zytnicki
date Thu, 14 Mar 2013 05:37:08 -0400
parents 769e306b7933
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 <tool id="plotGenomeCoverage" name="plot genome coverage">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 <description>Get the coverage of a genome. </description>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 <command interpreter="python"> ../Java/Python/plotGenomeCoverage.py -i $formatType.inputFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
4 #if $formatType.FormatInputFileName == 'bed':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
5 -f bed
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 #elif $formatType.FormatInputFileName == 'gff':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 -f gff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 #elif $formatType.FormatInputFileName == 'gff2':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 -f gff2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 #elif $formatType.FormatInputFileName == 'gff3':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 -f gff3
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 #elif $formatType.FormatInputFileName == 'sam':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 -f sam
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 #elif $formatType.FormatInputFileName == 'gtf':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 -f gtf
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 -r $reference
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 -o $outputFile
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 </command>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 <inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 <conditional name="formatType">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 <param name="FormatInputFileName" type="select" label="Input File Format">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 <option value="bed">bed</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 <option value="gff">gff</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 <option value="gff2">gff2</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 <option value="gff3">gff3</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 <option value="sam">sam</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31 <option value="gtf">gtf</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 <when value="bed">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34 <param name="inputFileName" format="bed" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36 <when value="gff">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 <param name="inputFileName" format="gff" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 <when value="gff2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42 <when value="gff3">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45 <when value="sam">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 <param name="inputFileName" format="sam" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48 <when value="gtf">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53 <param name="reference" type="data" label="reference Fasta File" format="fasta"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54 </inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 <outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 <data format="png" name="outputFile" label="[plotGenomeCoverage] Output File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 </outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 <help>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 </help>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 </tool>