# HG changeset patch
# User gregory-minevich
# Date 1349727160 14400
# Node ID 6572c40a8505dfbd424fbc70fda0d7e98ad9ae0d
# Parent  4892b1ac6739c0b3928c61072d8b956a4cd12fb0
Uploaded

diff -r 4892b1ac6739 -r 6572c40a8505 bcftools_view.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_view.xml	Mon Oct 08 16:12:40 2012 -0400
@@ -0,0 +1,163 @@
+<tool id="bcftools_view" name="bcftools view" version="0.0.1">
+    <description>Converts BCF format to VCF format</description>
+    <requirements>
+        <requirements type="package">samtools</requirements>
+    </requirements>
+    <command interpreter="python">
+        bcftools_view.py bcftools view 
+            #if str( $A ) == "true": 
+                -A
+            #end if
+            #if str( $b ) == "true":
+                -b
+            #end if
+	    #if $D.seq_dictionary == "true":
+                -D "$D.input"
+	    #end if
+            #if str( $F ) == "true":
+                -F
+	    #end if
+            #if str( $G ) == "true":
+                -G
+	    #end if
+            #if str( $N ) == "true":
+                -N
+	    #end if
+            #if str( $S ) == "true":
+                -S
+	    #end if
+            #if str( $u)  == "true":
+                -u
+	    #end if
+            #if str( $c ) == "true":
+                -c
+	    #end if
+            #if str( $e ) == "true":
+                -e
+	    #end if
+            #if str( $g ) == "true":
+                -g
+	    #end if
+            #if $i.alt_indel_snp_ratio == "true":
+                -i $i.ratio
+	    #end if
+            #if $p.variant_filter == "true":
+                -p $p.float_value
+	    #end if
+            #if $t.mutation_rate == "true":
+                -t $t.rate
+	    #end if
+            #if str( $v ) == "true":
+                -v
+	    #end if	
+	$input
+        > $output
+    </command>
+    <inputs>
+        <param name="input" type="data" format="bcf" label="Choose a bcf file to view" />
+        <param name="A" type="select" label="Retain all possible alternate alleles at variant sites">
+            <option value="true">Yes</option>
+            <option value="false" selected="true">No</option>
+        </param>
+        <param name="b" type="select" label="Output in the BCF format. The default is VCF.">
+            <option value="true">Yes</option>
+            <option value="false" selected="true">No</option>
+        </param>
+        <conditional name="D">
+            <param name="seq_dictionary" type="select" label="Sequence dictionary (list of chromosome names) for VCF->BCF conversion.">
+                <option value="true">Yes</option>
+                <option value="false" selected="true">No</option>
+            </param>
+            <when value="true">
+                <param name="input" type="data" format="tabular" label="Sequence dictionary" />
+            </when>
+        </conditional>
+        <param name="F" type="select" label="Indicate PL is generated by r921 or before (ordering is different).">
+            <option value="true">Yes</option>
+            <option value="false" selected="true">No</option>
+        </param>
+        <param name="G" type="select" label="Suppress all individual genotype information.">
+            <option value="true">Yes</option>
+            <option value="false" selected="true">No</option>
+        </param>
+        <param name="N" type="select" label="Skip sites where the REF field is not A/C/G/T">
+            <option value="true">Yes</option>
+            <option value="false" selected="true">No</option>
+        </param>
+        <param name="S" type="select" label="The input is VCF instead of BCF.">
+            <option value="true">Yes</option>
+            <option value="false" selected="true">No</option>
+        </param>
+        <param name="u" type="select" label="Uncompressed BCF output.">
+            <option value="true">Yes</option>
+            <option value="false" selected="true">No</option>
+        </param>
+        <param name="c" type="select" label="Call variants using Bayesian inference. Automatically performs max-likelihood inference only">
+            <option value="true" selected="true">Yes</option>
+            <option value="false">No</option>
+        </param>
+        <param name="e" type="select" label="Perform max-likelihood inference only, including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT.">
+            <option value="true">Yes</option>
+            <option value="false" selected="true">No</option>
+        </param>
+        <param name="g" type="select" label="Call per-sample genotypes at variant sites">
+            <option value="true" selected="true">Yes</option>
+            <option value="false">No</option>
+        </param>
+        <conditional name="i">
+            <param name="alt_indel_snp_ratio" type="select" label="Use alternate INDEL-to-SNP mutation rate, default 0.15.">
+                <option value="true">Yes</option>
+                <option value="false" selected="true">No</option>
+            </param>
+            <when value="true">
+                <param name="ratio" type="float" label="Ratio (float)" value="0.15" />
+            </when>
+        </conditional>
+        <conditional name="p">
+            <param name="variant_filter" type="select" >
+                <option value="true">Yes</option>
+                <option value="false" selected="true">No</option>
+            </param>
+            <when value="true">
+                <param name="float_value" type="float" label="Float" value="0.5" />
+            </when>
+        </conditional>
+	<conditional name="t">
+            <param name="mutation_rate" type="select" label="Specify scaled mutation rate for variant calling, default is 0.001.">
+                <option value="true">Yes</option>
+                <option value="false" selected="true">No</option>
+            </param>
+            <when value="true">
+                <param name="rate" type="float" label="Mutation Rate (float)" value="0.001" />
+            </when>
+        </conditional>
+        <param name="v" type="select" label="Output variant sites only.">
+            <option value="true" selected="true">Yes</option>
+            <option value="false">No</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+    <help>
+**What it does:** 
+
+This tool converts BCF files into VCF files using BCFtools view from the SAMtools set of utilities:
+
+http://samtools.sourceforge.net/samtools.shtml#4
+
+------
+
+**Citation:**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
+
+If you use this tool within Galaxy, please cite `Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert.  CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)`__
+
+    .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html
+
+Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.)
+
+    </help>
+</tool>