Mercurial > repos > bgruening > deeptools
diff computeGCBias.xml @ 18:5ea8782d650c draft
Uploaded
author | bgruening |
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date | Mon, 03 Feb 2014 13:44:35 -0500 |
parents | 16310f8b24d5 |
children | 69ff16ba27bd |
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--- a/computeGCBias.xml Sat Dec 21 14:26:06 2013 -0500 +++ b/computeGCBias.xml Mon Feb 03 13:44:35 2014 -0500 @@ -1,8 +1,9 @@ -<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.2"> +<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.3"> <description>to see whether your samples should be normalized for GC bias</description> <expand macro="requirements" /> <expand macro="stdio" /> <macros> + <token name="@BINARY@">computeGCBias</token> <import>deepTools_macros.xml</import> </macros> <command> @@ -24,10 +25,11 @@ --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt #end if + #if str(region).strip() != '': + --region 'region' + #end if + #if $advancedOpt.showAdvancedOpt == "yes": - #if str($advancedOpt.region.value) != '': - --region '$advancedOpt.region' - #end if --sampleSize '$advancedOpt.sampleSize' --regionSize '$advancedOpt.regionSize' @@ -56,6 +58,9 @@ <param name="fragmentLength" type="integer" value="300" min="1" label="Fragment length used for the sequencing" help ="If paired-end reads are used, the fragment length is computed from the BAM file."/> + + <expand macro="region_limit_operation" /> + <conditional name="advancedOpt"> <param name="showAdvancedOpt" type="select" label="Show advanced options" > <option value="no" selected="true">no</option> @@ -63,10 +68,6 @@ </param> <when value="no" /> <when value="yes"> - <param name="region" type="text" value="" - label="Region of the genome to limit the operation to" - help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" /> - <param name="sampleSize" type="integer" value="50000000" min="1" label="Number of sampling points to be considered" /> @@ -131,6 +132,11 @@ .. image:: $PATH_TO_IMAGES/QC_GCplots_input.png +You can find more details in the `computeGCBias wiki`_. + +.. _computeGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias + + **Output files**: - Diagnostic plot @@ -145,8 +151,6 @@ ----- -.. class:: infomark - @REFERENCES@ </help>