Mercurial > repos > galaxyp > openms_featurefindersuperhirn

annotate OMSSAAdapter.patch @ 14:ac6991743c11 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author galaxyp
date Fri, 06 Nov 2020 20:16:56 +0000
parents c42075bb5123
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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11
c42075bb5123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
1 --- OMSSAAdapter.xml 2020-06-16 15:51:40.315400730 +0200
c42075bb5123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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2 +++ /tmp/OMSSAAdapter.xml 2020-06-16 15:50:23.536086074 +0200
c42075bb5123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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3 @@ -22,6 +22,7 @@
c42075bb5123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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diff changeset
4 mkdir database &&
c42075bb5123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
5 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
c42075bb5123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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diff changeset
6
c42075bb5123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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7 +makeblastdb -dbtype prot -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
c42075bb5123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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8 ## Main program call
c42075bb5123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
9
c42075bb5123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
10 set -o pipefail &&