diff correctGCBias.xml @ 0:09b65c12a75a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/correctGCBias.xml	Sat Aug 03 13:42:12 2013 -0400
@@ -0,0 +1,112 @@
+<tool id="correctGCBias" name="correctGCBias" version="1.0">
+  <description>
+  </description>
+  <requirements>
+    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="0.1">ucsc_tools</requirement>
+  </requirements>
+  <command>
+  correctGCBias
+  --bamfile '$bamInput'
+  --species '$species'
+  --GCbiasFrequenciesFile $GCbiasFrequenciesFile
+  
+  #if $source.ref_source=="history":
+    --genome $source.input1
+  #else:
+    --genome "${source.input1_2bit.fields.path}"
+  #end if
+  
+  #if $advancedOpt.showAdvancedOpt == "yes":
+    #if str($advancedOpt.region.value) != '':
+      --region '$advancedOpt.region'
+    #end if
+    
+    --binSize '$advancedOpt.binSize'  
+  #end if
+  
+  #set newoutFileName="corrected."+str($outFileFormat)
+  
+  --correctedFile $newoutFileName; mv $newoutFileName $outFileName
+
+  </command>
+
+  <inputs>
+  
+  <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
+  
+  <param name="bamInput" format="bam" type="data" label="Input BAM file" help="The BAM file must be sorted and indexed."/>
+  
+  <param name="species" type="text" value="" label="Species name abbreviation" />
+  
+  <conditional name="source">
+    <param name="ref_source" type="select" label="Reference genome">
+        <option value="cached">locally cached</option>
+        <option value="history">in your history</option>
+    </param>
+    <when value="cached">
+        <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact your Galaxy team">
+            <options from_data_table="deepTools_seqs" />
+        </param>
+    </when>
+    <when value="history">
+        <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
+    </when>
+  </conditional>
+     
+  <param name="outFileFormat" type="select" label="File format of the output">
+    <option value="bam">bam</option>
+    <option value="bw">bigwig</option>
+    <option value="bg">bedgraph</option>
+  </param>
+  
+  <conditional name="advancedOpt">
+    <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+        <option value="no" selected="true">no</option>
+        <option value="yes">yes</option>
+      </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 &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
+           
+           <param name="binSize" type="integer" value="50" min="1" 
+             label="Bin size in bp"
+             help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
+      </when>
+  </conditional>
+  </inputs>
+  
+  <outputs>
+    <data format="bam" name="outFileName">
+    <change_format>
+        <when input="outFileFormat" value="bw" format="bigwig" />
+        <when input="outFileFormat" value="bam" format="bam" />
+        <when input="outFileFormat" value="bg" format="bedgraph" />
+    </change_format>
+    </data>
+  </outputs>
+  <help>
+
+**What it does**
+
+Computes the GC bias ussing Benjamini's method [citation]. The resulting GC
+bias can later be used to plot the bias or to correct the bias.
+
+-----
+
+.. class:: infomark
+
+Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_.
+
+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+
+
+.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _Fidel Ramirez: [e-mail]
+
+  </help>
+  
+</tool>