Mercurial > repos > saskia-hiltemann > igv_screenshot
comparison igvscreenshot.xml @ 0:aad38011de33 draft default tip
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author | saskia-hiltemann |
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date | Tue, 28 Jul 2015 11:16:53 -0400 |
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-1:000000000000 | 0:aad38011de33 |
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1 <tool id="igvscreenshot" name="Take an IGV screenshot" version="1.2"> | |
2 | |
3 <description>specifying tracks and a genomic location</description> | |
4 | |
5 <requirements> | |
6 <requirement type="package" version="2.3.57">igv</requirement> | |
7 </requirements> | |
8 | |
9 | |
10 <command interpreter="bash"> | |
11 igvscreenshot.sh | |
12 --build $reference | |
13 #for $i, $t in enumerate( $tracks ) | |
14 --track ${t.inputfile} | |
15 --ftype ${t.inputfile.extension} | |
16 --view ${t.view} | |
17 --viewaspairs ${t.viewaspairs} | |
18 #if not $t.trackname <!-- validator for empty field does not seem to work within a repeat, so this is the workaround --> | |
19 #set $tracklabel = "noname" | |
20 #else | |
21 #set $tracklabel = $t.trackname | |
22 #end if | |
23 --label $tracklabel | |
24 #if $t.inputfile.extension == "bam" | |
25 --index $t.inputfile.metadata.bam_index | |
26 #else | |
27 --index "none" | |
28 #end if | |
29 #end for | |
30 --region "$region" | |
31 </command> | |
32 | |
33 | |
34 <inputs> | |
35 <!-- parameter examples, see https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax for descriptions --> | |
36 | |
37 <param name="reference" type="select" label="Select Build"> | |
38 <option value="hg18"> hg18 </option> | |
39 <option value="hg19"> hg19 </option> | |
40 </param> | |
41 | |
42 <!-- file from history --> | |
43 <repeat name="tracks" title="Track" min="1"> | |
44 <param name="inputfile" type="data" format="bam,vcf,bed,gtf,gff" label="Select input file" help="choose input file from history"/> | |
45 <param name="trackname" type="text" size="100" value="track label" label="Track Label" > | |
46 <sanitizer> | |
47 <valid initial="default"> | |
48 <add preset="string.printable"/> | |
49 <remove value=" "/> | |
50 </valid> | |
51 <mapping initial="none"> | |
52 <add source=" " target="_"/> | |
53 </mapping> | |
54 </sanitizer> | |
55 </param> | |
56 <param name="view" type="select" label="View settings of track" > | |
57 <option value="collapse" > collapsed </option> | |
58 <option value="expand" > expanded </option> | |
59 <option value="squish" > squished </option> | |
60 </param> | |
61 <param name="viewaspairs" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="view as pairs?" help="optional setting for paired-end data"/> | |
62 | |
63 </repeat> | |
64 <!-- text field parameter --> | |
65 <param name="region" type="text" size="100" value="chr:start-end" label="Enter region to visualise in IGV, format chr:start-end" help="to show multiple regions in a single image, use comma-separated list of regions, e.g. chr1:0-100,chr2:100-200"/> | |
66 | |
67 </inputs> | |
68 | |
69 | |
70 <outputs> | |
71 <data format="png" name="outputfile" from_work_dir="screenshot.png" label="IGV screenshot of region ${region} on ${on_string}"/> | |
72 </outputs> | |
73 | |
74 <help> | |
75 This tool will create an IGV screenshot of the desired location(s) with the desired tracks. | |
76 | |
77 Tracks may be bam, vcf, bed, gff or gtf format. | |
78 | |
79 Multiple regions may be specified (comma-separated) | |
80 | |
81 | |
82 | |
83 </help> | |
84 </tool> |