Mercurial > repos > iuc > kofamscan
changeset 1:23494763e39e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
| author | iuc |
|---|---|
| date | Wed, 16 Feb 2022 09:25:13 +0000 |
| parents | 24adf43898ec |
| children | 95c71179a054 |
| files | kofamscan.xml test-data/profilesTyp2.tar.gz |
| diffstat | 2 files changed, 21 insertions(+), 3 deletions(-) [+] |
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--- a/kofamscan.xml Fri Jan 15 10:48:52 2021 +0000 +++ b/kofamscan.xml Wed Feb 16 09:25:13 2022 +0000 @@ -2,7 +2,7 @@ <description>gene function annotation based on KEGG orthology and HMM</description> <macros> <token name="@TOOL_VERSION@">1.3.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="reportannotation" token_selected=""> <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/> </xml> @@ -14,9 +14,12 @@ <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command> <command detect_errors="exit_code"><![CDATA[ ## preprocessing -mkdir 'profile' && +mkdir ./profile && +mkdir ./temp_extract && #if $p_cond.p_sel == 'compressed' - tar -xf '${p_cond.p}' -C 'profile' && + tar -xf '${p_cond.p}' -C temp_extract && + find ./temp_extract/ -name '*.hmm' -exec mv {} ./profile \; && + find ./temp_extract/ -name '*.hal' -exec mv {} ./profile \; && #elif $p_cond.p_sel == 'hmm' ## input files require prefix 'K' and file extension '.hmm' #for $i, $current in enumerate($p_cond.p) @@ -201,6 +204,21 @@ </assert_contents> </output> </test> + <!-- #5 --> + <test expect_num_outputs="1"> + <param name="query" value="query.fasta"/> + <conditional name="p_cond"> + <param name="p_sel" value="compressed"/> + <param name="p" value="profilesTyp2.tar.gz"/> + </conditional> + <param name="k" value="ko"/> + <output name="out_result"> + <assert_contents> + <has_n_lines n="5"/> + <has_text_matching expression=".+sp\|P00329\|ADH1_MOUSE.+"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark