diff merge_cut_up_clustering.xml @ 2:21ccf9548e2c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"

--- a/merge_cut_up_clustering.xml	Fri Jul 01 14:16:08 2022 +0000
+++ b/merge_cut_up_clustering.xml	Thu Jul 07 08:33:59 2022 +0000
@@ -1,32 +1,36 @@
-<tool id="concoct_merge_cut_up_clustering" name="CONCOCT: merge cut clusters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>into the original</description>
+<tool id="concoct_merge_cut_up_clustering" name="CONCOCT: Merge cut clusters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>and assign concensus clusters for the original contigs</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-python '$__tool_directory__/merge_cut_up_clustering.py'
---input '$input'
---output '$output'
+merge_cutup_clustering.py
+    '$cutup_clustering_result'
+    > '$output'
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="tabular" label="Tabular file containng cut up contigs"/>
+        <param name="cutup_clustering_result" type="data" format="csv" label="Clusters generated by CONCOCT"/>
     </inputs>
     <outputs>
-        <data name="output" format="tabular"/>
+        <data name="output" format="csv"/>
     </outputs>
     <tests>
         <!-- default settings -->
         <test expect_num_outputs="1">
-            <param name="input" value="input_merge_clusters.tabular" ftype="tabular"/>
-            <output name="output" file="output_merge_clusters.tabular" ftype="tabular"/>
+            <param name="cutup_clustering_result" value="clusters.csv" ftype="csv"/>
+            <output name="output" ftype="csv">
+                <assert_contents>
+                    <has_size value="6923"/>
+                    <has_text text="contig-21000001,39"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
 **What it does**
 
-Accepts a tbular file containing clusters output by the CONCOCT metagenome binning tool
-and produces a tabular file of the original contigs, with consecutive slices merged.
+This tool merges the clustering created by concoct by looking at cluster assignments per contig part and assigning a concensus cluster for the original contig. The output contains a header line and contig_id and cluster_id per line, separated by a comma.
 
 @HELP_OVERVIEW@
     ]]></help>