Mercurial > repos > mvdbeek > igv_take_screenshots
changeset 9:c357862a2927 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
| author | mvdbeek |
|---|---|
| date | Mon, 03 Jul 2017 11:36:19 -0400 |
| parents | ff0fb6dde58e |
| children | afb3f4c224d4 |
| files | igv_make_screenshots.xml |
| diffstat | 1 files changed, 5 insertions(+), 2 deletions(-) [+] |
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--- a/igv_make_screenshots.xml Mon Jul 03 10:58:06 2017 -0400 +++ b/igv_make_screenshots.xml Mon Jul 03 11:36:19 2017 -0400 @@ -15,6 +15,7 @@ cat '$load_session' > load_session.txt && echo snapshotDirectory "\$PWD" >> load_session.txt && cat load_session.txt '$script_file' '$exit_session' > igv_script.txt && + ## gives the cluster a bit of time to actually create the symlinks ... ughs sleep 10s && python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height && cp '$igv_session' '$igv_session_out' && @@ -66,6 +67,7 @@ ]]></configfile> <configfile name="load_session"> load igv_session.xml +preference SAM.SHOW_SOFT_CLIPPED $show_softclippped </configfile> <configfile name="exit_session"> exit @@ -84,9 +86,10 @@ </sanitizer> </param> </repeat> + <param name="show_softclippped" type="boolean" label="Show softclipped bases?" truevalue="true" falsevalue="false" checked="true"/> <param name="script_file" type="data" format="txt" label="Select a IGV script with regions for which to take screenshots"/> - <param name="width" label="Select the screenshot width" type="integer" min="640" value="1080"/> - <param name="height" label="Select the screenshot height" type="integer" min="800" value="1920"/> + <param name="width" label="Select the screenshot width" type="integer" min="800" value="1920"/> + <param name="height" label="Select the screenshot height" type="integer" min="640" value="1080"/> </inputs> <outputs> <data name="igv_session_out" format="xml"/>