changeset 0:bdd0cb7fbedf draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_macros.xml	Thu Aug 14 11:46:32 2014 -0400
@@ -0,0 +1,27 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="0.1.19">samtools</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command>@EXECUTABLE@ 2>&amp;1 | head -n 3 | tail -n 1</version_command>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+            <regex match="Error:" />
+            <regex match="Exception:" />
+        </stdio>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btp352</citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_view.xml	Thu Aug 14 11:46:32 2014 -0400
@@ -0,0 +1,94 @@
+<tool id="bcfview" name="bcftoolsView" version="0.1.19">
+    <description>Convert, filter, subset VCF/BCF files</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">bcftools</token>
+        <import>bcftools_macros.xml</import>
+    </macros>
+    <command>
+        @EXECUTABLE@ view
+            $A
+            $varsitesonly
+            $snpcalling
+            ##$F 
+            $G
+            $N
+            $e
+            $g
+
+            #if str( $output_format ) == "bcf":
+                -b
+            #end if
+
+            -D $seq_dict
+
+            -i $ratio
+            -t $rate
+
+            $input
+            &gt; $output
+
+    </command>
+    <inputs>
+        <param name="input" type="data" format="bcf,vcf" label="Choose a bcf file to view" />
+        <param name="output_format" type="select" label="Choose the output format" help="-b">
+            <option value="vcf" selected="true">VCF</option>
+            <option value="bcf">BCF</option>
+        </param>
+
+        <param name="seq_dict" type="data" format="tabular" optional="True" label="List of chromosome names for conversion" help="(-D)" />
+
+        <param name="ratio" type="float" label="Use alternate INDEL-to-SNP mutation rate" value="-1" help="defaults to 0.15 (-i)" />
+        <param name="rate" type="float" label="Mutation rate for variant calling" value="0.001" help="default to 0.001 (-t)" />
+
+        <param name="A" type="boolean" truevalue="-A" falsevalue="" checked="False"
+             label="Retain all possible alternate alleles at variant sites" help="-A" />
+        <param name="varsitesonly" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Output Potential Variant Sites Only" help="-v"/>
+        <param name="snpcalling" type="boolean" truevalue="-c" falsevalue="" checked="false" label="SNP calling" help="Forces -e the max-likelihood inference parameter. (-c)"/>
+        <!--param name="F" type="boolean" truevalue="-F" falsevalue="" checked="False"
+            label="Indicate PL is generated by r921 or before (ordering is different)" help="-F" /-->
+        <param name="G" type="boolean" truevalue="-G" falsevalue="" checked="False"
+            label="Suppress all individual genotype information" help="-G" />
+        <param name="N" type="boolean" truevalue="-N" falsevalue="" checked="False"
+            label="Skip sites where the REF field is not A/C/G/T" help="-N" />
+        <param name="e" type="boolean" truevalue="-e" falsevalue="" checked="False"
+            label="Perform max-likelihood inference only"
+            help="Including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT. (-e)" />
+        <param name="g" type="boolean" truevalue="-g" falsevalue="" checked="True"
+            label="Call per-sample genotypes at variant sites" help="-g" />
+    </inputs>
+
+    <outputs>
+        <data format="bcf" name="output">
+            <change_format>
+                <when input="output_format" value="vcf" format="vcf" />
+            </change_format>
+        </data>
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help>
+<![CDATA[
+**BCFTools View**
+
+VCF/BCF conversion, view, subset and filter VCF/BCF files.
+
+
+**Input format**
+
+`BCF files <http://www.1000genomes.org/wiki/analysis/variant-call-format/bcf-binary-vcf-version-2/>`_
+
+------
+
+**Outputs**
+
+VCF or BCF files
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Aug 14 11:46:32 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="samtools" version="0.1.19">
+      <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>