Mercurial > repos > galaxyp > openms_peakpickerhires

annotate OMSSAAdapter.patch @ 8:146b59d2d3e5 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
author galaxyp
date Wed, 04 Nov 2020 13:04:26 +0000
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146b59d2d3e5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
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1 --- OMSSAAdapter.xml 2020-06-16 15:51:40.315400730 +0200
146b59d2d3e5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
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2 +++ /tmp/OMSSAAdapter.xml 2020-06-16 15:50:23.536086074 +0200
146b59d2d3e5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
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3 @@ -22,6 +22,7 @@
146b59d2d3e5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
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4 mkdir database &&
146b59d2d3e5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
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5 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
146b59d2d3e5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
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6
146b59d2d3e5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
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7 +makeblastdb -dbtype prot -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
146b59d2d3e5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
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8 ## Main program call
146b59d2d3e5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
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9
146b59d2d3e5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
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diff changeset
10 set -o pipefail &&