diff trycycler_partition.xml @ 1:4688ae3b49b5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"

--- a/trycycler_partition.xml	Thu Feb 11 19:23:50 2021 +0000
+++ b/trycycler_partition.xml	Sat Feb 13 17:29:03 2021 +0000
@@ -1,10 +1,10 @@
-<tool id='trycycler_partition' name='Trycycler partition' version='@TOOL_VERSION@' profile='21.01'>
+<tool id='trycycler_partition' name='Trycycler partition' version='@TOOL_VERSION@' profile='20.01'>
     <description>assign the reads to the clusters</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 'partitions'
@@ -27,61 +27,53 @@
             mv '$fullpath/4_reads.fastq' 'partitions/partition_${number}.fastq' &&
         #end for
         echo 'bye!'
-    ]]></command>
+    ]]>    </command>
     <inputs>
-        <param name='input_cluster' type='data' 
-            format='fasta' multiple='true' label='Cluster datasets' 
-            help='Clustered contigs (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_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='input_cluster' type='data' format='fasta' multiple='true' label='Cluster datasets' help='Clustered contigs (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_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>
         <collection name='partitions' type='list' label='${tool.name} on ${on_string}'>
-            <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='partitions'/>        
+            <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='partitions' />
         </collection>
     </outputs>
     <tests>
         <test>
-            <param name='input_cluster' value='reconciled_cluster_01.fasta'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_aligned_len' value='1000'/>
-            <param name='min_read_cov' value='90'/>
+            <param name='input_cluster' value='reconciled_cluster_01.fasta' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_aligned_len' value='1000' />
+            <param name='min_read_cov' value='90' />
             <output_collection name='partitions' type='list' count='1'>
-                <element name='partition_01' file='partition_01.fastq' ftype='fastq'/>
+                <element name='partition_01' file='partition_01.fastq' ftype='fastq' />
             </output_collection>
         </test>
         <test>
-            <param name='input_cluster' value='reconciled_cluster_01.fasta'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_aligned_len' value='1200'/>
-            <param name='min_read_cov' value='95'/>
+            <param name='input_cluster' value='reconciled_cluster_01.fasta' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_aligned_len' value='1200' />
+            <param name='min_read_cov' value='95' />
             <output_collection name='partitions' type='list' count='1'>
-                <element name='partition_01' file='partition_02.fastq' ftype='fastq'/>
+                <element name='partition_01' file='partition_02.fastq' ftype='fastq' />
             </output_collection>
         </test>
         <test>
-            <param name='input_cluster' value='reconciled_cluster_01.fasta'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_aligned_len' value='900'/>
-            <param name='min_read_cov' value='93'/>
+            <param name='input_cluster' value='reconciled_cluster_01.fasta' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_aligned_len' value='900' />
+            <param name='min_read_cov' value='93' />
             <output_collection name='partitions' type='list' count='1'>
-                <element name='partition_01' file='partition_03.fastq' ftype='fastq'/>
+                <element name='partition_01' file='partition_03.fastq' ftype='fastq' />
             </output_collection>
         </test>
         <test>
-            <param name='input_cluster' value='reconciled_cluster_01.fasta'/>
-            <param name='reads' value='reads.fastq.gz'/>
-            <param name='min_aligned_len' value='1000'/>
-            <param name='min_read_cov' value='90'/>
+            <param name='input_cluster' value='reconciled_cluster_01.fasta' />
+            <param name='reads' value='reads.fastq.gz' />
+            <param name='min_aligned_len' value='1000' />
+            <param name='min_read_cov' value='90' />
             <output_collection name='partitions' type='list' count='1'>
-                <element name='partition_01' file='partition_04.fastq' ftype='fastq'/>
+                <element name='partition_01' file='partition_04.fastq' ftype='fastq' />
             </output_collection>
         </test>
     </tests>
@@ -115,6 +107,6 @@
 .. class:: infomark
 
 @PIPELINE@
-    ]]></help>
-    <expand macro='citations'/>
+    ]]>    </help>
+    <expand macro='citations' />
 </tool>