Mercurial > repos > yufei-luo > s_mart

annotate SMART/galaxy/getExons.xml @ 34:529e3e6a0954

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author m-zytnicki
date Tue, 30 Apr 2013 14:35:27 -0400
parents 0ab839023fe4
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="getExons" name="get exons">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 <description>Get the exons of a set of transcripts.</description>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 <command interpreter="python">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
4 ../Java/Python/getExons.py -i $formatType.inputFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
5 #if $formatType.FormatInputFileName == 'bed':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 -f bed
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 #elif $formatType.FormatInputFileName == 'gff':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 -f gff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 #elif $formatType.FormatInputFileName == 'gff2':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 -f gff2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 #elif $formatType.FormatInputFileName == 'gff3':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 -f gff3
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 #elif $formatType.FormatInputFileName == 'sam':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 -f sam
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 #elif $formatType.FormatInputFileName == 'gtf':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 -f gtf
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 #if $optionSelect.Value == "Yes":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 -s $optionSelect.selectValue
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 -o $outputFileGff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 </command>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 <inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 <conditional name="formatType">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 <param name="FormatInputFileName" type="select" label="Input File Format">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 <option value="bed">bed</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 <option value="gff">gff</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31 <option value="gff2">gff2</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32 <option value="gff3">gff3</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 <option value="sam">sam</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34 <option value="gtf">gtf</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36 <when value="bed">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 <param name="inputFileName" format="bed" 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="gff">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 <param name="inputFileName" format="gff" 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="gff2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43 <param name="inputFileName" format="gff2" 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="gff3">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 <param name="inputFileName" format="gff3" 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="sam">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 <param name="inputFileName" format="sam" 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 <when value="gtf">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 <conditional name="optionSelect">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 <param name="Value" type="select" label="select some of the exons (like '1,2,5..-3,-1')">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 <option value="Yes">Yes</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 <option value="No" selected="true">No</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 <when value="Yes">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 <param name="selectValue" type="text" value="None" label="select option" help="like '1,2,5..-3,-1'"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64 <when value="No">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 </inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69 <outputs>
31
0ab839023fe4 Uploaded
m-zytnicki
parents: 18
diff changeset
70 <data format="gff3" name="outputFileGff" label="[getExons -> gff3] Output File"/>
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 </outputs>
15
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
72 <tests>
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
73 <test>
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
74 <param name="FormatInputFileName" value="gtf" />
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
75 <param name="inputFileName" value="genes.gtf" />
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
76 <param name="Value" value="No"/>
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
77 <output name="outputFileGff" file="exp_getExons.gff3" />
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
78 </test>
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
79 </tests>
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
80 </tool>