# HG changeset patch
# User sanbi-uwc
# Date 1505897559 14400
# Node ID e4504b37b5c8cd9a1d0db29c60433ddba054eec3
# Parent  58b5fe349997a8bb415e496df90a91e1c07cc2ed
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0

diff -r 58b5fe349997 -r e4504b37b5c8 lofreq_call.xml
--- a/lofreq_call.xml	Fri Sep 08 03:37:38 2017 -0400
+++ b/lofreq_call.xml	Wed Sep 20 04:52:39 2017 -0400
@@ -30,6 +30,9 @@
         --def-nm-q "$DefNmQ"
         --min-cov "$MinCov"
         --max-depth "$MaxDepth"
+        --sig "$Sig"
+        --bonf "$Bonf"
+        --force-overwrite
         $merge_mapping_quality
         #if $sq_vcf and str($sq_vcf) != '':
           -S "$sq_vcf"
@@ -70,7 +73,7 @@
         <param name="MaxMq" type="integer" label="Cap mapping quality at " value="0" help="Cap mapping quality at [INT]" />
         <param name="DefNmQ" type="integer" label="If >= 0, then replace non-match base qualities with this default value [-1] " value="0" help="   If >= 0, then replace non-match base qualities with this default value [-1]" />
         <param name="MinCov" type="integer" label="Test only positions having at least this coverage " value="1" help="(note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)" />
-        <param name="MaxDepth" type="integer" label=" Cap coverage at this depth" value="1000000" help="Cap coverage at this depth [1000000] [INT]" />
+        <param name="MaxDepth" type="integer" label="Cap coverage at this depth" value="1000000" help="Cap coverage at this depth [1000000] [INT]" />
 
         <param name="merge_mapping_quality" type="boolean" truevalue="" falsevalue="--no-mq" checked="true" label="Don't merge mapping quality in LoFreq's model"/>
         <param format="vcf" name="sq_vcf" type="data" optional="true" label="Ignore variants in this vcf file for source quality computation."/>
@@ -79,15 +82,11 @@
             <option value="--only-indels">Only call indels; no SNVs</option>
         </param>
 
+        <param name="Sig" type="integer" label="P-Value cutoff / significance level [0.010000]" value="0.010000" help="P-Value cutoff / significance level [0.010000]" />
+        <param name="Bonf" type="text" label="Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']" value="dynamic" help="Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']" />
+
         <param name="misc" type="select" display="checkboxes" multiple="true" label="Misc Options">
-            <option value="--src-qual">Enable computation of source quality</option>
-            <option value="--sig">P-Value cutoff / significance level [0.010000]</option>
-            <option value="--bonf">Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']</option>
             <option value="--illumina-1.3">Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded</option>
-            <option value="--use-orphan">Count anomalous read pairs (i.e. where mate is not aligned properly)</option>
-            <option value="--plp-summary-only">No variant calling. Just output pileup summary per column</option>
-            <option value="--no-default-filter">Don't run default 'lofreq filter' automatically after calling variants</option>
-            <option value="--force-overwrite">Overwrite any existing output</option>
             <option value="--verbose">Be verbose</option>
         </param>