# HG changeset patch
# User iuc
# Date 1613237521 0
# Node ID 189e837009c96787cb865d675f3261a02b63a796
# Parent  c767a45616d0c7b6b10028c4f0061a3b9838c0ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"

diff -r c767a45616d0 -r 189e837009c9 trycycler_cluster.xml
--- a/trycycler_cluster.xml	Thu Feb 11 19:26:49 2021 +0000
+++ b/trycycler_cluster.xml	Sat Feb 13 17:32:01 2021 +0000
@@ -1,10 +1,10 @@
-<tool id='trycycler_cluster' name='Trycycler cluster' version='@TOOL_VERSION@' profile='21.01'>
+<tool id='trycycler_cluster' name='Trycycler cluster' version='@TOOL_VERSION@' profile='20.01'>
     <description>cluster the contigs of your input assemblies into per-replicon groups</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro='edam_ontology'/>
-    <expand macro='requirements'/>
+    <expand macro='edam_ontology' />
+    <expand macro='requirements' />
     <version_command>trycycler --version</version_command>
     <command detect_errors='exit_code'><![CDATA[
         #import re
@@ -23,77 +23,67 @@
         mv initial_clusters/contigs.phylip '$output_phylip' &&
         mv initial_clusters/contigs.newick '$output_newick' && 
         python3 '$__tool_directory__/trycycler.py' 'cluster' 'initial_clusters'
-    ]]></command>
+    ]]>    </command>
     <inputs>
-        <param name='assemblies' type='data' 
-            format='fasta,fasta.gz' multiple='true' label='Assembled sequences datasets' 
-            help='Input assemblies whose contigs will be clustered (multiple FASTA files)' />
-        <param name='reads' type='data' 
-            format='fastq,fastq.gz' label='Long-read datasets' 
-            help='Long reads (FASTQ format) used to generate the assemblies' />
-        <param argument='--min_contig_len' type='integer' 
-            min='100' max='5000' value='1000' label='Minimun contig length' 
-            help='Contigs shorter than this are thrown out on the assumption that they are either incomplete or spurious. The default value is 1000, as plasmids smaller than that are very rare.' />
-        <param argument='--min_contig_depth' type='float' 
-            min='0.01' max='1' value='0.1' label='Minimun contig depth' 
-            help='This controls how Trycycler filters out contigs with a low read depth. It is a multiple of the mean read depth for the assembly. For example, if an assembly has a mean depth of 90x and this setting is 0.1 (the default), then any contig with depth lower that x9 will be removed.'/> 
-        <param argument='--distance' type='float' 
-            min='0.001' max='0.1' value='0.01' label='Mash distance threshold' 
-            help='This is the Mash distance threshold used when defining clusters, and the default threshold is 0.01. Smaller thresholds (e.g. 0.005) can result in a larger number of tighter clusters. Larger thresholds (e.g. 0.02) can result in a smaller number of looser clusters.' />
+        <param name='assemblies' type='data' format='fasta,fasta.gz' multiple='true' label='Assembled sequences datasets' help='Input assemblies whose contigs will be clustered (multiple FASTA files)' />
+        <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read datasets' help='Long reads (FASTQ format) used to generate the assemblies' />
+        <param argument='--min_contig_len' type='integer' min='100' max='5000' value='1000' label='Minimun contig length' help='Contigs shorter than this are thrown out on the assumption that they are either incomplete or spurious. The default value is 1000, as plasmids smaller than that are very rare.' />
+        <param argument='--min_contig_depth' type='float' min='0.01' max='1' value='0.1' label='Minimun contig depth' help='This controls how Trycycler filters out contigs with a low read depth. It is a multiple of the mean read depth for the assembly. For example, if an assembly has a mean depth of 90x and this setting is 0.1 (the default), then any contig with depth lower that x9 will be removed.' />
+        <param argument='--distance' type='float' min='0.001' max='0.1' value='0.01' label='Mash distance threshold' help='This is the Mash distance threshold used when defining clusters, and the default threshold is 0.01. Smaller thresholds (e.g. 0.005) can result in a larger number of tighter clusters. Larger thresholds (e.g. 0.02) can result in a smaller number of looser clusters.' />
     </inputs>
     <outputs>
-        <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip'/>
-        <data name='output_newick' format='newick' label='${tool.name} on ${on_string}: newick'/>
+        <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip' />
+        <data name='output_newick' format='newick' label='${tool.name} on ${on_string}: newick' />
         <collection name='initial_clusters' type='list' label='${tool.name} on ${on_string}'>
-            <discover_datasets pattern='__designation_and_ext__' format='fasta' directory='initial_clusters'/>
+            <discover_datasets pattern='__designation_and_ext__' format='fasta' directory='initial_clusters' />
         </collection>
     </outputs>
     <tests>
         <test>
-            <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <output name='output_phylip' file='contigs_01.phylip'/>
-            <output name='output_newick' file='contigs_01.newick'/>
+            <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' />
+            <param name='reads' value='reads.fastq.gz' />
+            <output name='output_phylip' file='contigs_01.phylip' />
+            <output name='output_newick' file='contigs_01.newick' />
             <output_collection name='initial_clusters' type='list' count='2'>
-                <element name='cluster_01' file='cluster_01.fasta' ftype='fasta' lines_diff='20'/>
+                <element name='cluster_01' file='cluster_01.fasta' ftype='fasta' lines_diff='20' />
             </output_collection>
         </test>
         <test>
-            <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_contig_len' value='900'/>
-            <param name='min_contig_depth' value='0.05'/>
-            <param name='distance' value='0.05'/>
-            <output name='output_phylip' file='contigs_02.phylip'/>
-            <output name='output_newick' file='contigs_02.newick'/>
+            <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_contig_len' value='900' />
+            <param name='min_contig_depth' value='0.05' />
+            <param name='distance' value='0.05' />
+            <output name='output_phylip' file='contigs_02.phylip' />
+            <output name='output_newick' file='contigs_02.newick' />
             <output_collection name='initial_clusters' type='list' count='2'>
-                <element name='cluster_01' file='cluster_02.fasta' ftype='fasta' lines_diff='20'/>
+                <element name='cluster_01' file='cluster_02.fasta' ftype='fasta' lines_diff='20' />
             </output_collection>
         </test>
         <test>
-            <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_contig_len' value='850'/>
-            <param name='min_contig_depth' value='0.01'/>
-            <param name='distance' value='0.09'/>
-            <output name='output_phylip' file='contigs_03.phylip'/>
-            <output name='output_newick' file='contigs_03.newick'/>
+            <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_contig_len' value='850' />
+            <param name='min_contig_depth' value='0.01' />
+            <param name='distance' value='0.09' />
+            <output name='output_phylip' file='contigs_03.phylip' />
+            <output name='output_newick' file='contigs_03.newick' />
             <output_collection name='initial_clusters' type='list' count='2'>
-                <element name='cluster_01' file='cluster_03.fasta' ftype='fasta' lines_diff='20'/>
+                <element name='cluster_01' file='cluster_03.fasta' ftype='fasta' lines_diff='20' />
             </output_collection>
         </test>
         <test>
-            <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_contig_len' value='1100'/>
-            <param name='min_contig_depth' value='0.02'/>
-            <param name='distance' value='0.07'/>
-            <output name='output_phylip' file='contigs_04.phylip'/>
-            <output name='output_newick' file='contigs_04.newick'/>
+            <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_contig_len' value='1100' />
+            <param name='min_contig_depth' value='0.02' />
+            <param name='distance' value='0.07' />
+            <output name='output_phylip' file='contigs_04.phylip' />
+            <output name='output_newick' file='contigs_04.newick' />
             <output_collection name='initial_clusters' type='list' count='2'>
-                <element name='cluster_01' file='cluster_04.fasta' ftype='fasta' lines_diff='20'/>
+                <element name='cluster_01' file='cluster_04.fasta' ftype='fasta' lines_diff='20' />
             </output_collection>
-        </test>        
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
@@ -144,6 +134,6 @@
 .. class:: infomark
 
 @PIPELINE@
-    ]]></help>
-    <expand macro='citations'/>
+    ]]>    </help>
+    <expand macro='citations' />
 </tool>