# HG changeset patch
# User iuc
# Date 1714078671 0
# Node ID 2eb7932e91a37bff509d4780d2816d226b717ed2
# Parent  c3c46f14c7a454305c7d521f38ddfdcc3a5696fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 431ba943dcd0a584a64f28924396f3508c84f6b9

diff -r c3c46f14c7a4 -r 2eb7932e91a3 kofamscan.xml
--- a/kofamscan.xml	Mon Apr 22 14:41:54 2024 +0000
+++ b/kofamscan.xml	Thu Apr 25 20:57:51 2024 +0000
@@ -1,8 +1,8 @@
-<tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
     <description>gene function annotation based on KEGG orthology and HMM</description>
     <macros>
         <token name="@TOOL_VERSION@">1.3.0</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">3</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>
@@ -95,8 +95,8 @@
             <param argument="-T" type="integer" value="1" label="Set threshold scale" help="The score thresholds will be multiplied by this value."/>
             <conditional name="f_cond">
                 <param name="f_sel" type="select" label="Select output format">
-                    <option value="detail" selected="true">Details for each hit (including hits below threshold) (detail)</option>
-                    <option value="detail-tsv">Tab separeted values for detail format (detail-tsv)</option>
+                    <option value="detail">Details for each hit (including hits below threshold) (detail)</option>
+                    <option value="detail-tsv" selected="true">Tab separeted values for detail format (detail-tsv)</option>
                     <option value="mapper">KEGG Mapper compatible format (mapper)</option>
                     <option value="mapper-one-line">KEGG Mapper compatible format, but all hit KOs are listed in one line (mapper-oneline)</option>
                 </param>
@@ -333,4 +333,4 @@
     <citations>
         <citation type="doi">10.1093/bioinformatics/btz859</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff -r c3c46f14c7a4 -r 2eb7932e91a3 tool-data/kofam_subset.loc.sample
--- a/tool-data/kofam_subset.loc.sample	Mon Apr 22 14:41:54 2024 +0000
+++ b/tool-data/kofam_subset.loc.sample	Thu Apr 25 20:57:51 2024 +0000
@@ -1,2 +1,1 @@
-#value<tab>name<tab>kofam_value
-subset.hal	SUBSET	test_value
\ No newline at end of file
+#value<tab>name<tab>kofam_value
\ No newline at end of file