# HG changeset patch
# User iuc
# Date 1613237387 0
# Node ID e59bee4565b3343eeb55c7effbcf6f729575855a
# Parent  93c6a7423090473fec805d86e225a9408a04912b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"

diff -r 93c6a7423090 -r e59bee4565b3 trycycler_consensus.xml
--- a/trycycler_consensus.xml	Thu Feb 11 19:24:35 2021 +0000
+++ b/trycycler_consensus.xml	Sat Feb 13 17:29:47 2021 +0000
@@ -1,10 +1,10 @@
-<tool id='trycycler_consensus' name='Trycycler consensus' version='@TOOL_VERSION@' profile='21.01'>
+<tool id='trycycler_consensus' name='Trycycler consensus' version='@TOOL_VERSION@' profile='20.01'>
     <description>generate a consensus contig sequence for each cluster</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[
         mkdir -p 'selected_cluster' &&
@@ -19,70 +19,55 @@
             --min_read_cov $min_read_cov
             --threads \${GALAXY_SLOTS:-2} &&
             mv 'selected_cluster/7_final_consensus.fasta' $consensus
-    ]]></command>
+    ]]>    </command>
     <inputs>
-        <param name='cluster_all_seqs' type='data' 
-            format='fasta' label='Reconciled cluster' 
-            help='Reconciled sequences file' />
-        <param name='reconcile_msa' type='data' 
-            format='fasta' label='Reconcile msa' 
-            help='Multiple sequence alignment file' />
-        <param name='partition_reads' type='data' 
-            format='fastq' label='Partition reads' 
-            help='Partitioned reads' />
-        <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='--linear' type='boolean' 
-            truevalue='--linear' falsevalue='' 
-            label='Input contigs are not circular' 
-            help='Use this option if your input contigs are not circular. It will disable the circularisation-correction steps in Trycycler reconcile.' />
-        <param argument='--min_aligned_len' type='integer' min='500' max='3500' 
-            value='1000' label='Min bases aligned' 
-            help='Reads with less than this many bases aligned (default = 1000) will be ignored.' />
-        <param argument='--min_read_cov' type='integer' min='0' max='100' 
-            value='90' label='Min read length covered by alignments' 
-            help='Reads with less than this percentage of their length covered by alignments (default = 90.0) will be ignored.' />
+        <param name='cluster_all_seqs' type='data' format='fasta' label='Reconciled cluster' help='Reconciled sequences file' />
+        <param name='reconcile_msa' type='data' format='fasta' label='Reconcile msa' help='Multiple sequence alignment file' />
+        <param name='partition_reads' type='data' format='fastq' label='Partition reads' help='Partitioned reads' />
+        <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='--linear' type='boolean' truevalue='--linear' falsevalue='' label='Input contigs are not circular' help='Use this option if your input contigs are not circular. It will disable the circularisation-correction steps in Trycycler reconcile.' />
+        <param argument='--min_aligned_len' type='integer' min='500' max='3500' value='1000' label='Min bases aligned' help='Reads with less than this many bases aligned (default = 1000) will be ignored.' />
+        <param argument='--min_read_cov' type='integer' min='0' max='100' value='90' label='Min read length covered by alignments' help='Reads with less than this percentage of their length covered by alignments (default = 90.0) will be ignored.' />
     </inputs>
     <outputs>
-        <data name='consensus' format='fasta' label='${tool.name} on ${on_string}'/>
+        <data name='consensus' format='fasta' label='${tool.name} on ${on_string}' />
     </outputs>
     <tests>
         <test>
-            <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta'/>
-            <param name='reconcile_msa' value='aligned_cluster_01.fasta'/>
-            <param name='partition_reads' value='partition_01.fastq'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_aligned_len' value='1200'/>
-            <param name='min_read_cov' value='95'/>
-            <output name='consensus' file='consensus_sequence_01.fasta'/>
+            <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta' />
+            <param name='reconcile_msa' value='aligned_cluster_01.fasta' />
+            <param name='partition_reads' value='partition_01.fastq' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_aligned_len' value='1200' />
+            <param name='min_read_cov' value='95' />
+            <output name='consensus' file='consensus_sequence_01.fasta' />
         </test>
         <test>
-            <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta'/>
-            <param name='reconcile_msa' value='aligned_cluster_02.fasta'/>
-            <param name='partition_reads' value='partition_01.fastq'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_aligned_len' value='1100'/>
-            <param name='min_read_cov' value='90'/>
-            <output name='consensus' file='consensus_sequence_02.fasta'/>
+            <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta' />
+            <param name='reconcile_msa' value='aligned_cluster_02.fasta' />
+            <param name='partition_reads' value='partition_01.fastq' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_aligned_len' value='1100' />
+            <param name='min_read_cov' value='90' />
+            <output name='consensus' file='consensus_sequence_02.fasta' />
         </test>
         <test>
-            <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta'/>
-            <param name='reconcile_msa' value='aligned_cluster_03.fasta'/>
-            <param name='partition_reads' value='partition_01.fastq'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_aligned_len' value='1300'/>
-            <param name='min_read_cov' value='97'/>
-            <output name='consensus' file='consensus_sequence_03.fasta'/>
+            <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />
+            <param name='reconcile_msa' value='aligned_cluster_03.fasta' />
+            <param name='partition_reads' value='partition_01.fastq' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_aligned_len' value='1300' />
+            <param name='min_read_cov' value='97' />
+            <output name='consensus' file='consensus_sequence_03.fasta' />
         </test>
         <test>
-            <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta'/>
-            <param name='reconcile_msa' value='aligned_cluster_03.fasta'/>
-            <param name='partition_reads' value='partition_01.fastq'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_aligned_len' value='1000'/>
-            <param name='min_read_cov' value='87'/>
-            <output name='consensus' file='consensus_sequence_04.fasta'/>
+            <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />
+            <param name='reconcile_msa' value='aligned_cluster_03.fasta' />
+            <param name='partition_reads' value='partition_01.fastq' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_aligned_len' value='1000' />
+            <param name='min_read_cov' value='87' />
+            <output name='consensus' file='consensus_sequence_04.fasta' />
         </test>
     </tests>
     <help><![CDATA[
@@ -140,6 +125,6 @@
 .. class:: infomark
 
 @PIPELINE@
-    ]]></help>
-    <expand macro='citations'/>
+    ]]>    </help>
+    <expand macro='citations' />
 </tool>