--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pileup_to_vcf.xml	Mon Feb 18 11:32:50 2013 -0500
@@ -0,0 +1,112 @@
+<tool id="pileup_to_vcf" name="Pileup to VCF" version="2.0">
+  <description>Converts a pileup to VCF with filtering</description>
+  <command interpreter="python">pileup_to_vcf.py -i $input_file -o $output_file 
+    #if $min_cvrg.__str__  != '':
+      --min_coverage $min_cvrg 
+    #end if
+    #if $min_base_qual.__str__  != '':
+      --min_base_qual $min_base_qual
+    #end if
+    #if $min_var_pct.__str__  != '':
+      --min_allele_freq $min_var_pct 
+    #end if
+    #if $depth_as.__str__ != 'None':
+      --report_depth $depth_as
+    #end if
+    $allow_multiples
+    $snps_only
+    #if $cols.select_order == 'yes' :
+      #if $chrom_col.__str__  != '':
+        --chrom_col $chrom_col 
+      #end if
+      #if $pos_col.__str__  != '':
+        --pos_col $pos_col 
+      #end if
+      #if $ref_col.__str__  != '':
+        --ref_col $ref_col 
+      #end if
+      #if $cvrg_col.__str__  != '':
+        --coverage_col $cvrg_col 
+      #end if
+      #if $base_call_col.__str__  != '':
+        --base_call_col $base_call_col 
+      #end if
+      #if $base_qual_col.__str__  != '':
+        --base_qual_col $base_qual_col 
+      #end if
+    #end if
+  </command>
+  <inputs>
+    <param name="input_file" type="data" format="pileup,tabular" label="Source File" optional="false"/>
+    <conditional name="cols">
+      <param name="select_order" type="select" label="Set column positions for non-standard pileup">
+        <option value="no" selected="true">Use the default pileup columns</option>
+        <option value="yes">Select the column position that represents each pileup column</option>
+      </param>
+      <when value="no"/>
+      <when value="yes">
+        <param name="chrom_col" type="data_column" data_ref="input_file" label="Chromosome Column"/>
+        <param name="pos_col" type="data_column" data_ref="input_file" label="Position Column"/>
+        <param name="ref_col" type="data_column" data_ref="input_file" label="Reference Base Column"/>
+        <param name="cvrg_col" type="data_column" data_ref="input_file" label="Depth Column"/>
+        <param name="base_call_col" type="data_column" data_ref="input_file" label="Base Call Column"/>
+        <param name="base_qual_col" type="data_column" data_ref="input_file" label="Base Quality Column"/>
+      </when>
+    </conditional>
+    <param name="min_base_qual" type="integer" label="Minimum Base Quality" optional="true" value="20" help="Don't consider a read if the base call quality is below this threshold"/>
+    <param name="min_cvrg" type="integer" label="Minimum Coverage Depth" optional="true" value="5" help="Any position below the threshold will be omitted from the resulting VCF"/>
+    <param name="min_var_pct" type="float" label="Minimum Frequency of a Specific Allele" option="true" value="0.5" help="If an allele does not meet the minimum frequency it will be omitted from the resulting VCF."/>
+    <param name="allow_multiples" type="boolean" truevalue="-m" falsevalue="" chacked="true" label="Allow Multiple Alleles for a Position?" 
+           help="Multiple alleles may be output in the VCF if the allowable frequency is below 0.5, otherwise only one will be reported"/>
+    <param name="snps_only" type="boolean" truevalue="-s" falsevalue="" chacked="false" label="Only report SNPs, not indels" />
+    <param name="depth_as" type="select" label="Report DP and SAF with read coverage of" help="The reported read voverage depth: DP, and the calculation of specific allele frequency (SAF) of variants">
+      <option value="ref" selected="true">Reads at this position</option>
+      <option value="qual">Reads at this position taht pass the base call quality threshold</option>
+      <option value="all"></option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="vcf" metadata_source="input_file" name="output_file" />
+  </outputs>
+  <stdio>
+    <exit_code range="1:"  level="fatal"   description="Bad input dataset" />
+  </stdio>
+  <tests>
+    <test>
+      <param name="input_file" ftype="pileup" value="test.pileup" />
+      <param name="select_order" value="no"/>
+      <param name="min_base_qual" value="0"/>
+      <param name="min_cvrg" value="0"/>
+      <param name="min_var_pct" value=".1"/>
+      <param name="allow_multiples" value="True"/>
+      <param name="snps_only" value="False"/>
+      <param name="depth_as" value="ref"/>
+      <output name="output_file">
+        <assert_contents>
+            <has_text_matching expression="seq2\t156\t.\tA\tG,AAG\t.\tPASS\t.*" />
+            <has_text_matching expression="chr1\t158571283\t.\tA\tC,T\t.\tPASS\t.*" />
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="input_file" ftype="pileup" value="test.pileup" />
+      <param name="select_order" value="no"/>
+      <param name="min_base_qual" value="20"/>
+      <param name="min_cvrg" value="5"/>
+      <param name="min_var_pct" value=".1"/>
+      <param name="allow_multiples" value="True"/>
+      <param name="snps_only" value="False"/>
+      <param name="depth_as" value="ref"/>
+      <output name="output_file">
+        <assert_contents>
+            <has_text_matching expression="seq2\t156\t.\tA\tG,AAG\t.\tPASS\t.*" />
+            <has_text_matching expression="chr1\t158571283\t.\tA\tC\t.\tPASS\t.*" />
+        </assert_contents>
+      </output>
+    </test>
+
+  </tests>
+  <help>
+    Pileup to VCF converts the output of a pileup tool to a VCF representing any alleles that surpass a user specified frequency, optionally presenting multiple alleles for a given position if the allele frequency is set below 0.5.  This tool assumes that any filtering for base call quality and mapping quality has been done in previous processing.
+  </help>
+</tool>