# HG changeset patch
# User greg
# Date 1538752195 14400
# Node ID 4dc497887a5c178280d99170153ffe2409c360d2
# Parent  54dfcde738ad52756de77851fa100a169e4651d1
Uploaded

diff -r 54dfcde738ad -r 4dc497887a5c affy2vcf.xml
--- a/affy2vcf.xml	Fri Oct 05 10:58:29 2018 -0400
+++ b/affy2vcf.xml	Fri Oct 05 11:09:55 2018 -0400
@@ -7,17 +7,21 @@
 #set text_outputs_dir = 'text_outputs'
 mkdir $text_outputs_dir &&
 bcftools +affy2vcf.so
---fasta_ref '$reference_genome.fasta_ref'
+#if str($reference_genome_source_cond.reference_genome_source) == "history":
+    --fasta_ref '$reference_genome_source_cond.history_item'
+#else:
+    --fasta_ref '$reference_genome_source_cond.locally_cached_item'
+#end if
 --annot '$annot'
 --snp-posteriors '$text_outputs_dir/snp_posteriors.txt'
 --summary '$text_outputs_dir/summary.txt'
 --report '$text_outputs_dir/report.txt'
 --calls '$text_outputs_dir/calls.txt'
 --confidences '$text_outputs_dir/confidences.txt'
-#if str($output_gender_estimate_cond.output_gender_estimate) == "yes"
+#if str($output_gender_estimate) == "yes"
     --sex '$text_outputs_dir/gender_estimate.txt'
 #end if
-#if str($append_version_cond.append_version) == "no":
+#if str($append_version) == "no":
     --no-version
 #end if
 --output '$output'
@@ -26,16 +30,16 @@
     ]]></command>
     <inputs>
         <param name="annot" type="data" format="csv" label="Probeset annotation file" />
-        <conditional name="reference_genome">
-            <param name="source" type="select" label="Will you select a reference reference genome from your history or use a locally cached genome index?">
+        <conditional name="reference_genome_source_cond">
+            <param name="reference_genome_source" type="select" label="Will you select a reference reference genome from your history or use a locally cached genome index?">
                 <option value="history" selected="true">Use a reference genome from my history</option>
                 <option value="cached">Use a locally cached genome index</option>
             </param>
             <when value="history">
-                <param name="fasta_ref" type="data" format="fasta" label="Select reference genome" />
+                <param name="history_item" type="data" format="fasta" label="Select reference genome" />
             </when>
             <when value="cached">
-                <param name="fasta_ref" type="select" format="fasta" label="Fasta reference sequence">
+                <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence">
                     <options from_data_table="all_fasta">
                         <column name="name" index="1"/>
                         <column name="value" index="2"/>
@@ -46,22 +50,20 @@
                 </param>
             </when>
         </conditional>
-        <conditional name="output_gender_estimate_cond">
-            <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
-                <option value="no" selected="true">No</option>
-                <option value="yes">Yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes"/>
-        </conditional>
-        <conditional name="append_version_cond">
-            <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
-                <option value="no" selected="true">No</option>
-                <option value="yes">Yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes"/>
-        </conditional>
+        <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
+            <option value="no" selected="true">No</option>
+            <option value="yes">Yes</option>
+        </param>
+        <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
+            <option value="no" selected="true">No</option>
+            <option value="yes">Yes</option>
+        </param>
+        <param name="output_type" type="select" force_select="true" label="Select format for output?">
+            <option value="v" selected="true">Uncompressed VCF</option>
+            <option value="z">Compressed VCF</option>
+            <option value="u" selected="true">Uncompressed BCF</option>
+            <option value="b">Compressed BCF</option>
+        </param>
     </inputs>
     <outputs>
         <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}">