From 8fda22d17183b7dd59976c27d4e74ba4165d7a4e Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 25 Sep 2024 12:54:13 +0200
Subject: [PATCH 1/2] fix linter errors for structure harvester

---
 tools/structureharvester/.lint_skip             |  2 --
 tools/structureharvester/structureharvester.xml | 14 +++++++++-----
 2 files changed, 9 insertions(+), 7 deletions(-)
 delete mode 100644 tools/structureharvester/.lint_skip

diff --git a/tools/structureharvester/.lint_skip b/tools/structureharvester/.lint_skip
deleted file mode 100644
index 4d97c7e23e6..00000000000
--- a/tools/structureharvester/.lint_skip
+++ /dev/null
@@ -1,2 +0,0 @@
-InputsNameDuplicateOutput
-TestsExpectNumOutputs
diff --git a/tools/structureharvester/structureharvester.xml b/tools/structureharvester/structureharvester.xml
index 85cff2238a1..00085706825 100644
--- a/tools/structureharvester/structureharvester.xml
+++ b/tools/structureharvester/structureharvester.xml
@@ -1,7 +1,11 @@
-<tool id="structureharvester" name="structureHarvester" version="0.6.94">
+<tool id="structureharvester" name="structureHarvester" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>for parsing STRUCTURE outputs and for performing the Evanno method</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.6.94</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.6.94">structureharvester</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">structureharvester</requirement>
     </requirements>
     <version_command><![CDATA[
         structureHarvester.py --version
@@ -14,7 +18,7 @@
         structureHarvester.py --dir inputs/ --out . $evanno $clumpp &&
         mv summary.txt '$summary'
         #if $evanno
-            && mv evanno.txt $evanno
+            && mv evanno.txt '$evanno_out'
         #end if
         #if $clumpp
             && mkdir clumpp_indfile clumpp_popfile
@@ -29,7 +33,7 @@
     </inputs>
     <outputs>
         <data name="summary" format="txt" label="Structure Harvester summary"/>
-        <data name="evanno" format="txt" label="Evann method output">
+        <data name="evanno_out" format="txt" label="Evann method output">
             <filter>evanno</filter>
         </data>
         <collection name="clumpp_indfile" type="list" label="Clumpp K*.indfile">
@@ -42,7 +46,7 @@
         </collection>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="inputs" value="example_harvester_archive/Admix_run_001_f,example_harvester_archive/Admix_run_002_f,example_harvester_archive/Admix_run_004_f,example_harvester_archive/Admix_run_005_f,example_harvester_archive/Admix_run_007_f,example_harvester_archive/Admix_run_008_f,example_harvester_archive/K1ReRun_run_1_f,example_harvester_archive/K1ReRun_run_2_f" />
             <param name="evanno" value="false" />
             <param name="clumpp" value="true" />

From b6d29300d21ea9da6f27d2de29cc621416338c46 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 25 Sep 2024 13:09:05 +0200
Subject: [PATCH 2/2] add label default

---
 tools/structureharvester/structureharvester.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/structureharvester/structureharvester.xml b/tools/structureharvester/structureharvester.xml
index 00085706825..005d0733200 100644
--- a/tools/structureharvester/structureharvester.xml
+++ b/tools/structureharvester/structureharvester.xml
@@ -32,15 +32,15 @@
         <param argument="--clumpp" type="boolean" checked="false" truevalue="--clumpp" falsevalue="" label="Generates one K*.indfile for each value of K run, for use with CLUMPP." />
     </inputs>
     <outputs>
-        <data name="summary" format="txt" label="Structure Harvester summary"/>
-        <data name="evanno_out" format="txt" label="Evann method output">
+        <data name="summary" format="txt" label="${tool.name} on ${on_string}: Summary"/>
+        <data name="evanno_out" format="txt" label="${tool.name} on ${on_string}: Evann output">
             <filter>evanno</filter>
         </data>
-        <collection name="clumpp_indfile" type="list" label="Clumpp K*.indfile">
+        <collection name="clumpp_indfile" type="list" label="${tool.name} on ${on_string}: Clumpp K*.indfile">
             <filter>clumpp</filter>
             <discover_datasets pattern="__name__" format="txt" directory="clumpp_indfile" />
         </collection>
-        <collection name="clumpp_popfile" type="list" label="Clumpp K*.popfile">
+        <collection name="clumpp_popfile" type="list" label="${tool.name} on ${on_string}: Clumpp K*.popfile">
             <filter>clumpp</filter>
             <discover_datasets pattern="__name__" format="txt" directory="clumpp_popfile" />
         </collection>