Mercurial > repos > saskia-hiltemann > igv_screenshot
comparison igvscreenshot.xml @ 0:aad38011de33 draft default tip
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| author | saskia-hiltemann |
|---|---|
| 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> |