Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 30:9d6b4d2ca187 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0437e9e56f0af2ccfb5f119b0f290109807ed9b0-dirty
author mvdbeek
date Fri, 15 Jun 2018 14:01:18 -0400
parents dd61761307ca
children 474837e086cc
comparison
equal deleted inserted replaced
29:dd61761307ca 30:9d6b4d2ca187
7 #set $file_ext = $inputsection.input.extension 7 #set $file_ext = $inputsection.input.extension
8 #set $igv_ext = $file_ext if $file_ext != "gff3" else "gff" 8 #set $igv_ext = $file_ext if $file_ext != "gff3" else "gff"
9 #set $element_identifier = $inputsection.input.element_identifier 9 #set $element_identifier = $inputsection.input.element_identifier
10 #set $display_link = "{galaxy_url}/display_application/{dataset_id}/igv_{igv_ext}/local_default/None/data/galaxy_{dataset_id}.{file_ext}".format(galaxy_url=galaxy_url, dataset_id=dataset_id, igv_ext=igv_ext, file_ext=file_ext, user_id=user_id) 10 #set $display_link = "{galaxy_url}/display_application/{dataset_id}/igv_{igv_ext}/local_default/None/data/galaxy_{dataset_id}.{file_ext}".format(galaxy_url=galaxy_url, dataset_id=dataset_id, igv_ext=igv_ext, file_ext=file_ext, user_id=user_id)
11 ]]></token> 11 ]]></token>
12 <token name="@PATH@"><![CDATA[#set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)]]></token> 12 <token name="@PATH@"><![CDATA[
13 #import re
14 #set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)
15 ]]></token>
13 </macros> 16 </macros>
14 <requirements> 17 <requirements>
15 <requirement type="package" version="0.2.9">xvfbwrapper</requirement> 18 <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
16 <!-- TODO: uncomment when igv in conda 19 <!-- TODO: uncomment when igv in conda
17 <requirement type="package" version="2.3.93">igv</requirement> 20 <requirement type="package" version="2.3.93">igv</requirement>
55 #end for 58 #end for
56 </Resources> 59 </Resources>
57 #for $i, $inputsection in enumerate($inputfiles): 60 #for $i, $inputsection in enumerate($inputfiles):
58 #if $inputsection.input.is_of_type('bam') 61 #if $inputsection.input.is_of_type('bam')
59 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier) 62 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
60 @PATH 63 @PATH@
61 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width"> 64 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
62 ## First track is the coverage 65 ## First track is the coverage
63 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true"> 66 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
64 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/> 67 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
65 </Track> 68 </Track>