Mercurial > repos > jdv > canu

diff canu.xml @ 1:ed5df116fad3 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/canu commit da020fbee6e2bd91bc4a8d0850dc601db34ac82b-dirty
author jdv
date Sun, 15 Oct 2017 21:40:46 -0400
parents 7d87a6450883
children a5198537f8a2
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--- a/canu.xml	Wed Sep 06 12:24:44 2017 -0400
+++ b/canu.xml	Sun Oct 15 21:40:46 2017 -0400
@@ -25,11 +25,12 @@
         -p canu_galaxy
         -d out_dir
         useGrid=false
-        genomeSize=$genome_size
-        rawErrorRate=$raw_error_rate
-        correctedErrorRate=$corrected_error_rate
-        minReadLength=$min_read_length
-        minOverlapLength=$min_overlap
+        genomeSize=$genomeSize
+        rawErrorRate=$rawErrorRate
+        correctedErrorRate=$correctedErrorRate
+        minReadLength=$minReadLength
+        minOverlapLength=$minOverlapLength
+        corOutCoverage=$corOutCoverage
         minThreads=\${GALAXY_SLOTS:-1}
         maxThreads=\${GALAXY_SLOTS:-1}
         gnuplotTested=true
@@ -52,11 +53,12 @@
             <option value="-nanopore-corrected">nanopore corrected</option>
             <option value="-pacbio-corrected">pacbio corrected</option>
         </param>
-        <param name="genome_size" type="text" size="5" label="Estimated genome size (e.g. 80m, 15k, 2g)" />
-        <param name="raw_error_rate" type="float" value="0.500" min="0" max="1" size="5" label="Maximum raw overlap mismatch (0-1)" />
-        <param name="corrected_error_rate" type="float" value="0.144" min="0" max="1" size="5" label="Maximum corrected overlap mismatch (0-1)" />
-        <param name="min_read_length" type="integer" value="1000" min="1" size="5" label="Minimum read length" />
-        <param name="min_overlap" type="integer" value="500" min="1" size="5" label="Minimum overlap" />
+        <param argument="genomeSize" type="text" size="5" label="Estimated genome size (e.g. 80m, 15k, 2g)" />
+        <param argument="rawErrorRate" type="float" value="0.500" min="0" max="1" size="5" label="Maximum raw overlap mismatch (0-1)" />
+        <param argument="correctedErrorRate" type="float" value="0.144" min="0" max="1" size="5" label="Maximum corrected overlap mismatch (0-1)" />
+        <param argument="minReadLength" type="integer" value="1000" min="1" size="5" label="Minimum read length" />
+        <param argument="minOverlapLength" type="integer" value="500" min="1" size="5" label="Minimum overlap" />
+        <param argument="corOutCoverage" type="integer" value="40" min="1" size="5" label="Target coverage for corrected reads" />
 
     </inputs>
 
@@ -71,14 +73,8 @@
 
     <!-- ***************************************************************** -->
 
-    <!--
     <tests>
-        <test>
-            <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
-            <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
-        </test>
     </tests>
-    -->
 
     <!-- ***************************************************************** -->