Mercurial > repos > mvdbeek > igv_take_screenshots
changeset 30:9d6b4d2ca187 draft
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 |
| files | igv_make_screenshots.xml |
| diffstat | 1 files changed, 5 insertions(+), 2 deletions(-) [+] |
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--- a/igv_make_screenshots.xml Fri Jun 15 13:33:51 2018 -0400 +++ b/igv_make_screenshots.xml Fri Jun 15 14:01:18 2018 -0400 @@ -9,7 +9,10 @@ #set $element_identifier = $inputsection.input.element_identifier #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) ]]></token> - <token name="@PATH@"><![CDATA[#set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)]]></token> + <token name="@PATH@"><![CDATA[ +#import re +#set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension) +]]></token> </macros> <requirements> <requirement type="package" version="0.2.9">xvfbwrapper</requirement> @@ -57,7 +60,7 @@ #for $i, $inputsection in enumerate($inputfiles): #if $inputsection.input.is_of_type('bam') #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier) - @PATH + @PATH@ <Panel height="$inputsection.section_height" name="Panel${label}" width="$width"> ## First track is the coverage <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">