Mercurial > repos > iuc > colibread_commet

changeset 6:4daa32d21ea5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:55:07 +0000
parents d03353742508
children
files commet.xml macros.xml
diffstat 2 files changed, 18 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/commet.xml	Thu May 06 12:45:20 2021 +0000
+++ b/commet.xml	Sat Oct 05 19:55:07 2024 +0000
@@ -1,10 +1,11 @@
-<tool id="commet" name="Commet" version="24.7.14+galaxy0" profile="@PROFILE@">
+<tool id="commet" name="Commet" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>COmpare Multiple METagenomes</description>
     <macros>
+        <token name="@TOOL_VERSION@">24.7.14</token>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="24.7.14">commet</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">commet</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #for $i, $set in enumerate($sets):
@@ -45,29 +46,28 @@
         <param name="percentage_outputs" label="Generate percentage files" type="boolean" checked="false"/>
     </inputs>
     <outputs>
-        <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="Matrix plain with ${tool.name} on ${on_string}" >
+        <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="${tool.name} on ${on_string}: Matrix plain" >
             <filter>plain_outputs</filter>
         </data>
-        <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="Matrix percentage with ${tool.name} on ${on_string}" >
+        <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="${tool.name} on ${on_string}: Matrix percentage" >
             <filter>percentage_outputs</filter>
         </data>
-        <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="Matrix normalized with ${tool.name} on ${on_string}" >
+        <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="${tool.name} on ${on_string}: Matrix normalized" >
             <filter>normalized_outputs</filter>
         </data>
-        <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="Dendrogram ${tool.name} on ${on_string}" />
-        <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="Heatmap normalized with ${tool.name} on ${on_string}" >
+        <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="${tool.name} on ${on_string}: Dendrogram" />
+        <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="${tool.name} on ${on_string}: Heatmap normalized" >
             <filter>normalized_outputs</filter>
         </data>
-        <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="Heatmap percentage with ${tool.name} on ${on_string}" >
+        <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="${tool.name} on ${on_string}: Heatmap percentage" >
             <filter>percentage_outputs</filter>
         </data>
-        <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="Heatmap Plain with ${tool.name} on ${on_string}" >
+        <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="${tool.name} on ${on_string}: Heatmap Plain" >
             <filter>plain_outputs</filter>
         </data>
     </outputs>
     <tests>
-        <test>
-            <param name="input_type" value="list" />
+        <test expect_num_outputs="5">
             <repeat name="sets">
                 <param name="reads" value="commet/A.fa.gz" ftype="fasta.gz" />
             </repeat>
@@ -80,6 +80,11 @@
             <param name="plain_outputs" value="True"/>
             <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/>
             <output name="matrix_plain" file="commet/matrix_plain.csv"/>
+            <output name="heatmap_plain">
+                <assert_contents>
+                    <has_size size="1k"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
--- a/macros.xml	Thu May 06 12:45:20 2021 +0000
+++ b/macros.xml	Sat Oct 05 19:55:07 2024 +0000
@@ -1,11 +1,10 @@
 <macros>
-    <token name="@DISCOSNP_VERSION@">2.5.4</token>
 
-    <token name="@PROFILE@">20.01</token>
+    <token name="@PROFILE@">23.1</token>
 
     <xml name="discosnp_requirements">
         <requirements>
-            <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">discosnp</requirement>
         </requirements>
     </xml>