From 431ba943dcd0a584a64f28924396f3508c84f6b9 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 25 Apr 2024 22:48:26 +0200
Subject: [PATCH] kofamscan: remove entry from sample datatable (#5964)

* kofamscan: remove entry from sample datatable

and switch default to tabular output

* profile + bump
---
 tools/kofamscan/kofamscan.xml                     | 10 +++++-----
 tools/kofamscan/tool-data/kofam_subset.loc.sample |  3 +--
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/tools/kofamscan/kofamscan.xml b/tools/kofamscan/kofamscan.xml
index 645544c6d7a..027e90f9c7b 100644
--- a/tools/kofamscan/kofamscan.xml
+++ b/tools/kofamscan/kofamscan.xml
@@ -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 @@ $ap.f_cond.reportannotation
             <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 @@ More information are available on `GitHub <https://github.com/takaram/kofam_scan
     <citations>
         <citation type="doi">10.1093/bioinformatics/btz859</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/kofamscan/tool-data/kofam_subset.loc.sample b/tools/kofamscan/tool-data/kofam_subset.loc.sample
index 5eb6dc5cc94..46a545eff9b 100644
--- a/tools/kofamscan/tool-data/kofam_subset.loc.sample
+++ b/tools/kofamscan/tool-data/kofam_subset.loc.sample
@@ -1,2 +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