# HG changeset patch
# User iuc
# Date 1678878304 0
# Node ID a0713a10c9f614f3f554aa6e7ac6a0892d9e1713
# Parent  368cb4bef9d894faeec77273b0542de7d372928f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 91d5bae878afa54d8264c1ca89c79b2d26ef35ad

diff -r 368cb4bef9d8 -r a0713a10c9f6 drep_dereplicate.xml
--- a/drep_dereplicate.xml	Mon Jun 27 13:40:40 2022 +0000
+++ b/drep_dereplicate.xml	Wed Mar 15 11:05:04 2023 +0000
@@ -5,7 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.2.0">checkm-genome</requirement>
+        <requirement type="package" version="1.2.2">checkm-genome</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 @PREPARE_GENOMES@
@@ -56,6 +56,18 @@
             <expand macro="test_default_filtering_options"/>
             <expand macro="test_default_quality_assessment_options"/>
             <expand macro="test_default_comparison_clustering_options"/>
+            <expand macro="test_extra_weight_table_scoring_options"/>
+            <expand macro="test_default_warning_options"/>
+            <expand macro="test_default_select_drep_outputs"/>
+            <expand macro="test_log_output">
+                <has_text text="dRep dereplicate finished" />
+            </expand>
+        </test>
+        <test expect_num_outputs="8">
+            <expand macro="test_string_inputs"/>
+            <expand macro="test_default_filtering_options"/>
+            <expand macro="test_default_quality_assessment_options"/>
+            <expand macro="test_default_comparison_clustering_options"/>
             <expand macro="test_default_scoring_options"/>
             <expand macro="test_default_warning_options"/>
             <expand macro="test_default_select_drep_outputs"/>
diff -r 368cb4bef9d8 -r a0713a10c9f6 macros.xml
--- a/macros.xml	Mon Jun 27 13:40:40 2022 +0000
+++ b/macros.xml	Wed Mar 15 11:05:04 2023 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">3.3.0</token>
+    <token name="@TOOL_VERSION@">3.4.2</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="biotools">
@@ -271,6 +271,7 @@
             <param argument="--N50_weight" type="float" value=".5" label="Weight of log(genome N50)"/>
             <param argument="--size_weight" type="float" value="0" label="Weight of log(genome size)"/>
             <param argument="--centrality_weight" type="float" value="1" label="Weight of (centrality - S_ani)"/>
+            <param argument="--extra_weight_table" type="data" format="tabular" multiple="false" optional="true" label="Genome specific extra weight"/>
         </section>
     </xml>
     <xml name="test_default_scoring_options">
@@ -283,6 +284,17 @@
             <param name="centrality_weight" value="1"/>
         </section>
     </xml>
+    <xml name="test_extra_weight_table_scoring_options">
+        <section name="scoring">
+            <param name="completeness_weight" value="1"/>
+            <param name="contamination_weight" value="5"/>
+            <param name="strain_heterogeneity_weight" value="1"/>
+            <param name="N50_weight" value=".5" />
+            <param name="size_weight" value="0"/>
+            <param name="centrality_weight" value="1"/>
+            <param name="extra_weight_table" ftype="tabular" value="extra_weight_table_test"/>
+        </section>
+    </xml>
     <token name="@SCORING_OPTIONS@"><![CDATA[
     --completeness_weight $scoring.completeness_weight
     --contamination_weight $scoring.contamination_weight
@@ -290,6 +302,10 @@
     --N50_weight $scoring.N50_weight
     --size_weight $scoring.size_weight
     --centrality_weight $scoring.centrality_weight
+    #if str($extra_weight_table) != 'None'
+    	--extra_weight_table $extra_weight_table
+    #end if
+    
 ]]></token>
 
     <xml name="warning_options">
@@ -483,6 +499,8 @@
                         weight of log(genome N50) (default: 0.5)
   -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT
                         weight of log(genome size) (default: 0)
+  -extraW EXTRA_WEIGHT_TABLE, --extra_weight_table EXTRA_WEIGHT_TABLE
+  			Path to a tab-separated file with two-columns, no headers, listing genome and extra score to apply to that genome (optional)
 
 
 ]]></token>
diff -r 368cb4bef9d8 -r a0713a10c9f6 test-data/extra_weight_table_test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extra_weight_table_test	Wed Mar 15 11:05:04 2023 +0000
@@ -0,0 +1,5 @@
+a	1
+b	2
+c	3
+
+