Mercurial > repos > sanbi-uwc > lofreq
changeset 5:e4504b37b5c8 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0
author | sanbi-uwc |
---|---|
date | Wed, 20 Sep 2017 04:52:39 -0400 |
parents | 58b5fe349997 |
children | c208346da4be |
files | lofreq_call.xml |
diffstat | 1 files changed, 7 insertions(+), 8 deletions(-) [+] |
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--- 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>