Mercurial > repos > saskia-hiltemann > igv_screenshot
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/igvscreenshot.xml Tue Jul 28 11:16:53 2015 -0400 @@ -0,0 +1,84 @@ +<tool id="igvscreenshot" name="Take an IGV screenshot" version="1.2"> + + <description>specifying tracks and a genomic location</description> + + <requirements> + <requirement type="package" version="2.3.57">igv</requirement> + </requirements> + + + <command interpreter="bash"> + igvscreenshot.sh + --build $reference + #for $i, $t in enumerate( $tracks ) + --track ${t.inputfile} + --ftype ${t.inputfile.extension} + --view ${t.view} + --viewaspairs ${t.viewaspairs} + #if not $t.trackname <!-- validator for empty field does not seem to work within a repeat, so this is the workaround --> + #set $tracklabel = "noname" + #else + #set $tracklabel = $t.trackname + #end if + --label $tracklabel + #if $t.inputfile.extension == "bam" + --index $t.inputfile.metadata.bam_index + #else + --index "none" + #end if + #end for + --region "$region" + </command> + + + <inputs> + <!-- parameter examples, see https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax for descriptions --> + + <param name="reference" type="select" label="Select Build"> + <option value="hg18"> hg18 </option> + <option value="hg19"> hg19 </option> + </param> + + <!-- file from history --> + <repeat name="tracks" title="Track" min="1"> + <param name="inputfile" type="data" format="bam,vcf,bed,gtf,gff" label="Select input file" help="choose input file from history"/> + <param name="trackname" type="text" size="100" value="track label" label="Track Label" > + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <remove value=" "/> + </valid> + <mapping initial="none"> + <add source=" " target="_"/> + </mapping> + </sanitizer> + </param> + <param name="view" type="select" label="View settings of track" > + <option value="collapse" > collapsed </option> + <option value="expand" > expanded </option> + <option value="squish" > squished </option> + </param> + <param name="viewaspairs" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="view as pairs?" help="optional setting for paired-end data"/> + + </repeat> + <!-- text field parameter --> + <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"/> + + </inputs> + + + <outputs> + <data format="png" name="outputfile" from_work_dir="screenshot.png" label="IGV screenshot of region ${region} on ${on_string}"/> + </outputs> + + <help> +This tool will create an IGV screenshot of the desired location(s) with the desired tracks. + +Tracks may be bam, vcf, bed, gff or gtf format. + +Multiple regions may be specified (comma-separated) + + + + </help> +</tool> \ No newline at end of file