Mercurial > repos > iuc > kofamscan

changeset 1:23494763e39e draft

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"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(-) [+]
line wrap: on
line diff
--- 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
Binary file test-data/profilesTyp2.tar.gz has changed