Mercurial > repos > jdv > canu

changeset 2:a5198537f8a2 draft default tip

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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 22:29:50 -0400
parents ed5df116fad3
children
files canu.xml
diffstat 1 files changed, 15 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/canu.xml	Sun Oct 15 21:40:46 2017 -0400
+++ b/canu.xml	Sun Oct 15 22:29:50 2017 -0400
@@ -31,6 +31,13 @@
         minReadLength=$minReadLength
         minOverlapLength=$minOverlapLength
         corOutCoverage=$corOutCoverage
+        contigFilter="
+            ${contigFilter.minReads}
+            ${contigFilter.minLength}
+            ${contigFilter.singleReadSpan}
+            ${contigFilter.lowCovSpan}
+            ${contigFilter.lowCovDepth}
+        "
         minThreads=\${GALAXY_SLOTS:-1}
         maxThreads=\${GALAXY_SLOTS:-1}
         gnuplotTested=true
@@ -60,6 +67,14 @@
         <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" />
 
+        <section name="contigFilter" title="Contig Filters">
+            <param argument="minReads" type="integer" value="2" min="0" label="Minimum reads" />
+            <param argument="minLength" type="integer" value="0" min="0" label="Minimum length" />
+            <param argument="singleReadSpan" type="float" value="1.0" min="0.0" max="1.0" label="Maximum single read span (fraction)" />
+            <param argument="lowCovSpan" type="float" value="0.5" min="0.0" max="1.0" label="Low coverage span (fraction)" />
+            <param argument="lowCovDepth" type="integer" value="5" min="0" label="Low coverage depth" />
+        </section>
+
     </inputs>
 
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