| Previous changeset 0:2782bee7c5a6 (2021-12-02) Next changeset 2:2452952f7bc2 (2023-04-03) |
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Commit message:
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty" |
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modified:
rp2paths.xml |
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| diff -r 2782bee7c5a6 -r e3db7fb2c85e rp2paths.xml --- a/rp2paths.xml Thu Dec 02 12:27:28 2021 +0000 +++ b/rp2paths.xml Tue Feb 22 11:31:06 2022 +0000 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="rp2paths" name="RP2paths" version="1.4.3"> +<tool id="rp2paths" name="RP2paths" version="1.5.0"> <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> <requirements> - <requirement type="package" version="1.4.3">rp2paths</requirement> + <requirement type="package" version="1.5.0">rp2paths</requirement> </requirements> <stdio> <regex match="TIMEOUT:" level="fatal" /> @@ -9,17 +9,15 @@ <regex match="WARNING:" level="warning" /> </stdio> <command detect_errors="exit_code"><![CDATA[ - #from os import path as os_path - cd /tmp && - #set outFolder = os_path.basename(str($master_pathways)) - mkdir '$outFolder' && + mkdir out && python -m rp2paths all '$rp2_pathways' - --outdir '$outFolder' + --outdir out --timeout '$adv.timeout' && - cp '$outFolder'/compounds.txt '$compounds' && - cp '$outFolder'/out_paths.csv '$master_pathways' && - rm -rf $outFolder + if test -f "out/compounds.txt"; then + cp out/compounds.txt '$compounds'; + cp out/out_paths.csv '$master_pathways'; + fi ]]></command> <inputs> <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" /> |