Mercurial > repos > galaxyp > openms_consensusid

comparison generate-foo.sh @ 17:abffdfee3021 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
author galaxyp
date Mon, 22 Feb 2021 10:46:10 +0000
parents feebe2054e40
children f4be248c3d47
comparison
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16:01dbaf6a57e0 17:abffdfee3021
81 81
82 ctdtmp=$(mktemp) 82 ctdtmp=$(mktemp)
83 #echo python3 fill_ctd_clargs.py --ctd $ini $cli 83 #echo python3 fill_ctd_clargs.py --ctd $ini $cli
84 # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"]) 84 # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
85 # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli" 85 # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli"
86 eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp" 86 eval "python3 fill_ctd_clargs.py --ini_file $ini --ctd_file ctd/$tool_id.ctd $cli" > "$ctdtmp"
87 # echo $ctdtmp 87 # echo $ctdtmp
88 # >&2 cat $ctdtmp 88 # >&2 cat $ctdtmp
89 testtmp=$(mktemp) 89 testtmp=$(mktemp)
90 python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null 90 python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null
91 cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/' 91 cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'