# HG changeset patch
# User iuc
# Date 1613237158 0
# Node ID fa4e97daaf30d79436ed6bd93da0b0026a7a0a50
# Parent  deb7b00e877eb0b214be65d835bcfb85761e98fb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"

diff -r deb7b00e877e -r fa4e97daaf30 trycycler_subsample.xml
--- a/trycycler_subsample.xml	Thu Feb 11 19:20:35 2021 +0000
+++ b/trycycler_subsample.xml	Sat Feb 13 17:25:58 2021 +0000
@@ -1,10 +1,10 @@
-<tool id='trycycler_subsample' name='Trycycler subsample' version='@TOOL_VERSION@' profile='21.01'>
+<tool id='trycycler_subsample' name='Trycycler subsample' version='@TOOL_VERSION@' profile='20.01'>
     <description>make a maximally-independent read subsets of an appropiate depth for your genome</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 output_subsamples &&
@@ -17,34 +17,21 @@
             --min_read_depth $min_read_depth
             --threads \${GALAXY_SLOTS:-2}
             --out_dir output_subsamples
-    ]]></command>
+    ]]>    </command>
     <inputs>
-        <param name='reads' type='data' 
-            format='fastq,fastq.gz'  
-            label='Long-read dataset' help='--reads' />
-        <param argument='--count' type='integer' 
-            min='2' max='20' 
-            value='12' label='Number of subsampled reads set to output' 
-            help='The number of subsamples reads to make maximally-independent read subsets. The default is 12, a good number for most cases.' />
+        <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read dataset' help='--reads' />
+        <param argument='--count' type='integer' min='2' max='20' value='12' label='Number of subsampled reads set to output' help='The number of subsamples reads to make maximally-independent read subsets. The default is 12, a good number for most cases.' />
         <conditional name='option'>
-            <param name='genome' type='select' 
-                label='Provide an estimated genomoe size'
-                help='If you do not provide this, Trycycler subsample will run miniasm to quickly assemble your read set to get a size. This value is used to calculate read depths and does not need to be exact, e.g. 10% error is fine.' >
-                    <option value='true'>Provide estimeted genome size</option>
-                    <option value='false'>Run miniasm for estimating genome size</option>
+            <param name='genome' type='select' label='Provide an estimated genomoe size' help='If you do not provide this, Trycycler subsample will run miniasm to quickly assemble your read set to get a size. This value is used to calculate read depths and does not need to be exact, e.g. 10% error is fine.' >
+                <option value='true'>Provide estimeted genome size</option>
+                <option value='false'>Run miniasm for estimating genome size</option>
             </param>
-            <when value='false'/>
+            <when value='false' />
             <when value='true'>
-                <param argument='--genome_size' type='integer' 
-                    min='10000' max='15000000' 
-                    value='30000' label='Estimated total genome size' 
-                    help='An estimate of the isolate total genome size.' />
+                <param argument='--genome_size' type='integer' min='10000' max='15000000' value='30000' label='Estimated total genome size' help='An estimate of the isolate total genome size.' />
             </when>
         </conditional>
-        <param argument='--min_read_depth' type='integer' min='15' max='120' 
-            value='25' 
-            label='Minimum subset read depth' 
-            help='This is the minimum allowed read depth and also controls the subsampled depths. If is not provided, Trycycle decides what read depth each subset will be.' />
+        <param argument='--min_read_depth' type='integer' min='15' max='120' value='25' label='Minimum subset read depth' help='This is the minimum allowed read depth and also controls the subsampled depths. If is not provided, Trycycle decides what read depth each subset will be.' />
     </inputs>
     <outputs>
         <collection name='subsamples_fastq' type='list'>
@@ -53,76 +40,76 @@
     </outputs>
     <tests>
         <test>
-            <param name='reads' value='reads.fastq.gz'/>
+            <param name='reads' value='reads.fastq.gz' />
             <conditional name='option'>
-                <param name='genome' value='true'/>
-                <param name='genome_size' value='10000'/>
+                <param name='genome' value='true' />
+                <param name='genome_size' value='10000' />
             </conditional>
-            <param name='min_read_depth' value='20'/>
-            <param name='count' value='4'/>
+            <param name='min_read_depth' value='20' />
+            <param name='count' value='4' />
             <output_collection name='subsamples_fastq' type='list' count='4'>
-                <element name='sample_01' file='sample_01_01.fastq' ftype='fastq'/>
-                <element name='sample_02' file='sample_02_01.fastq' ftype='fastq'/>
-                <element name='sample_03' file='sample_03_01.fastq' ftype='fastq'/>
-                <element name='sample_04' file='sample_04_01.fastq' ftype='fastq'/>
+                <element name='sample_01' file='sample_01_01.fastq' ftype='fastq' />
+                <element name='sample_02' file='sample_02_01.fastq' ftype='fastq' />
+                <element name='sample_03' file='sample_03_01.fastq' ftype='fastq' />
+                <element name='sample_04' file='sample_04_01.fastq' ftype='fastq' />
             </output_collection>
         </test>
         <test>
-            <param name='reads' value='reads.fastq.gz'/>
+            <param name='reads' value='reads.fastq.gz' />
             <conditional name='option'>
-                <param name='genome' value='true'/>
-                <param name='genome_size' value='10000'/>
+                <param name='genome' value='true' />
+                <param name='genome_size' value='10000' />
             </conditional>
-            <param name='min_read_depth' value='22'/>
-            <param name='count' value='6'/>
+            <param name='min_read_depth' value='22' />
+            <param name='count' value='6' />
             <output_collection name='subsamples_fastq' type='list' count='6'>
-                <element name='sample_01' file='sample_01_02.fastq' ftype='fastq'/>
-                <element name='sample_02' file='sample_02_02.fastq' ftype='fastq'/>
-                <element name='sample_03' file='sample_03_02.fastq' ftype='fastq'/>
-                <element name='sample_04' file='sample_04_02.fastq' ftype='fastq'/>
-                <element name='sample_05' file='sample_05_02.fastq' ftype='fastq'/>
-                <element name='sample_06' file='sample_06_02.fastq' ftype='fastq'/>
+                <element name='sample_01' file='sample_01_02.fastq' ftype='fastq' />
+                <element name='sample_02' file='sample_02_02.fastq' ftype='fastq' />
+                <element name='sample_03' file='sample_03_02.fastq' ftype='fastq' />
+                <element name='sample_04' file='sample_04_02.fastq' ftype='fastq' />
+                <element name='sample_05' file='sample_05_02.fastq' ftype='fastq' />
+                <element name='sample_06' file='sample_06_02.fastq' ftype='fastq' />
             </output_collection>
         </test>
         <test>
-            <param name='reads' value='reads.fastq.gz'/>
+            <param name='reads' value='reads.fastq.gz' />
             <conditional name='option'>
-                <param name='genome' value='true'/>
-                <param name='genome_size' value='10000'/>
+                <param name='genome' value='true' />
+                <param name='genome_size' value='10000' />
             </conditional>
-            <param name='min_read_depth' value='25'/>
-            <param name='count' value='5'/>
+            <param name='min_read_depth' value='25' />
+            <param name='count' value='5' />
             <output_collection name='subsamples_fastq' type='list' count='5'>
-                <element name='sample_01' file='sample_01_03.fastq' ftype='fastq'/>
-                <element name='sample_02' file='sample_02_03.fastq' ftype='fastq'/>
-                <element name='sample_03' file='sample_03_03.fastq' ftype='fastq'/>
-                <element name='sample_04' file='sample_04_03.fastq' ftype='fastq'/>
-                <element name='sample_05' file='sample_05_03.fastq' ftype='fastq'/>
+                <element name='sample_01' file='sample_01_03.fastq' ftype='fastq' />
+                <element name='sample_02' file='sample_02_03.fastq' ftype='fastq' />
+                <element name='sample_03' file='sample_03_03.fastq' ftype='fastq' />
+                <element name='sample_04' file='sample_04_03.fastq' ftype='fastq' />
+                <element name='sample_05' file='sample_05_03.fastq' ftype='fastq' />
             </output_collection>
         </test>
         <test>
-            <param name='reads' value='reads.fastq.gz'/>
+            <param name='reads' value='reads.fastq.gz' />
             <conditional name='option'>
-                <param name='genome' value='true'/>
-                <param name='genome_size' value='10000'/>
+                <param name='genome' value='true' />
+                <param name='genome_size' value='10000' />
             </conditional>
-            <param name='min_read_depth' value='30'/>
-            <param name='count' value='12'/>
+            <param name='min_read_depth' value='30' />
+            <param name='count' value='12' />
             <output_collection name='subsamples_fastq' type='list' count='12'>
-                <element name='sample_01' file='sample_01_04.fastq' ftype='fastq'/>
-                <element name='sample_02' file='sample_02_04.fastq' ftype='fastq'/>
-                <element name='sample_03' file='sample_03_04.fastq' ftype='fastq'/>
-                <element name='sample_04' file='sample_04_04.fastq' ftype='fastq'/>
-                <element name='sample_05' file='sample_05_04.fastq' ftype='fastq'/>
-                <element name='sample_06' file='sample_06_04.fastq' ftype='fastq'/>
-                <element name='sample_07' file='sample_07_04.fastq' ftype='fastq'/>
-                <element name='sample_08' file='sample_08_04.fastq' ftype='fastq'/>
-                <element name='sample_09' file='sample_09_04.fastq' ftype='fastq'/>
-                <element name='sample_10' file='sample_10_04.fastq' ftype='fastq'/>
-                <element name='sample_11' file='sample_11_04.fastq' ftype='fastq'/>
-                <element name='sample_12' file='sample_12_04.fastq' ftype='fastq'/>
+                <element name='sample_01' file='sample_01_04.fastq' ftype='fastq' />
+                <element name='sample_02' file='sample_02_04.fastq' ftype='fastq' />
+                <element name='sample_03' file='sample_03_04.fastq' ftype='fastq' />
+                <element name='sample_04' file='sample_04_04.fastq' ftype='fastq' />
+                <element name='sample_05' file='sample_05_04.fastq' ftype='fastq' />
+                <element name='sample_06' file='sample_06_04.fastq' ftype='fastq' />
+                <element name='sample_07' file='sample_07_04.fastq' ftype='fastq' />
+                <element name='sample_08' file='sample_08_04.fastq' ftype='fastq' />
+                <element name='sample_09' file='sample_09_04.fastq' ftype='fastq' />
+                <element name='sample_10' file='sample_10_04.fastq' ftype='fastq' />
+                <element name='sample_11' file='sample_11_04.fastq' ftype='fastq' />
+                <element name='sample_12' file='sample_12_04.fastq' ftype='fastq' />
             </output_collection>
-        </test> 
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
@@ -153,6 +140,6 @@
 .. class:: infomark
 
 @PIPELINE@
-    ]]></help>
-    <expand macro='citations'/>
+    ]]>    </help>
+    <expand macro='citations' />
 </tool>