# HG changeset patch
# User paulgordon
# Date 1360615426 18000
# Node ID da1dba1da40aae95e7b831e6fa3975ef7e3b5f89
# Parent  59d3e3484f161b0d14a41793cdfa648e73328b2c
Uploaded

diff -r 59d3e3484f16 -r da1dba1da40a atlas2_indel.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/atlas2_indel.xml	Mon Feb 11 15:43:46 2013 -0500
@@ -0,0 +1,57 @@
+<tool id="atlas2_indel_1" name="Call indels using Atlas2">
+  <description></description>
+  <requirements>
+    <requirement type="package" version="1.4.1">freebayes</requirement>
+    <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements>
+  <command interpreter="ruby">
+    /export/achri_data/programs/Atlas2_v1.4.1/Atlas-Indel2/Atlas-Indel2.rb -b $bam_file -r /export/geno_tmp/achri/dbs/$refgenome\.fa -o $vcf_outfile
+    -p $max_pvalue -v $min_prop $platform 
+    #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
+       -B "${target_limit_type.input_target_bed}"
+    #end if
+    &amp;> /dev/null
+  </command>
+  <inputs>
+    <param name="bam_file" label="Mapped reads file (BAM)" type="data" format="bam" />
+    <param name="refgenome" type="genomebuild" label="Reference genome" help="against which indels will be called"/>
+    <param name="platform" label="Platform used for sequencing" type="select" display="radio">
+      <option value="-S" selected="true">SOLiD</option>
+      <option value="-I">Illumina</option>
+    </param>
+    <param name="max_pvalue" label="Maximum p-value to call a variant" type="float" min="0" value="0.01" max="1" help="0.01=~99% random exclusion"/>
+    <param name="min_prop" label="Minimum proportion of variants to make a call" type="float" min="0.01" value="0.1" max="1.0" />
+    <conditional name="target_limit_type">
+          <param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets">
+            <option value="do_not_limit" selected="True">Do not limit</option>
+            <option value="limit_by_target_file">Limit by target file</option>
+          </param>
+          <when value="do_not_limit">
+            <!-- Do nothing here -->
+          </when>
+          <when value="limit_by_target_file">
+            <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." />
+          </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data name="vcf_outfile" format="vcf" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="bam_file" value="test2" />
+      <param name="refgenome" value="hg19" />
+      <param name="platform" value="-S" />
+      <param name="max_pvalue" value="0.01" />
+      <param name="min_prop" value="0.1" />
+      <output name="vcf_outfile" file="sam_merge_out2.log" ftype="vcf" lines_diff="11"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+This tools uses the Atlas2 software to call indels in a way that accounts for the systematic error types of either SOLiD or Illumina sequencing. 
+It does NOT call SNPs. The output is a VCF file, and can be combined with SNP caller output to form a more complete picture of sequence variation.
+  </help>
+</tool>