Mercurial > repos > tduigou > rptools_rpcompletion
changeset 6:64ccaeec8554 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit df6ff93f58dcad0892d429597544cd674f9253ee-dirty
author | tduigou |
---|---|
date | Thu, 23 Oct 2025 14:39:36 +0000 |
parents | ec5e25d1a3f1 |
children | |
files | macros.xml rpcompletion.xml |
diffstat | 2 files changed, 27 insertions(+), 17 deletions(-) [+] |
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--- a/macros.xml Wed Oct 22 12:03:06 2025 +0000 +++ b/macros.xml Thu Oct 23 14:39:36 2025 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">6.6.6</token> + <token name="@TOOL_VERSION@">6.7.1</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> @@ -12,4 +12,4 @@ <organization name="BioRetroSynth" url="https://github.com/brsynth" /> </creator> </xml> -</macros> +</macros> \ No newline at end of file
--- a/rpcompletion.xml Wed Oct 22 12:03:06 2025 +0000 +++ b/rpcompletion.xml Thu Oct 23 14:39:36 2025 +0000 @@ -13,28 +13,38 @@ description="The sink file is empty or not found" /> </stdio> <command detect_errors="exit_code"><![CDATA[ + #import os + #if "TMPDIR" in os.environ + #set tmpdir=os.environ["TMPDIR"]/rr_cache + mkdir -p '$tmpdir' && + #else + #set tmpdir="." + #end if + #if str($sink.cond) == 'empty' echo '"Name","InChI"' > empty_sink.csv && #set sinkfile='empty_sink.csv' #else #set sinkfile=$sink.sinkfile #end if + python -m rptools.rpcompletion - '$rp2_pathways' - $sinkfile - '$rp2paths_compounds' - '$rp2paths_pathways' - completed_pathways - --upper_flux_bound '$adv.upper_flux_bound' - --lower_flux_bound '$adv.lower_flux_bound' - --max_subpaths_filter '$adv.max_subpaths_filter' - --chemical-space '$adv.chemical_space' - #if $adv.cofile - --cofactors '$adv.cofile' - #end if - #if not $sink.error_codes - --silent - #end if + '$rp2_pathways' + $sinkfile + '$rp2paths_compounds' + '$rp2paths_pathways' + completed_pathways + --upper_flux_bound '$adv.upper_flux_bound' + --lower_flux_bound '$adv.lower_flux_bound' + --max_subpaths_filter '$adv.max_subpaths_filter' + --chemical-space '$adv.chemical_space' + #if $adv.cofile + --cofactors '$adv.cofile' + #end if + #if not $sink.error_codes + --silent + #end if + --cache-dir '$tmpdir' ]]></command> <inputs> <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />