diff naive_variant_caller.xml @ 16:07e71cf6c8ef draft

planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c

--- a/naive_variant_caller.xml	Wed Feb 28 16:01:52 2018 -0500
+++ b/naive_variant_caller.xml	Tue Apr 03 10:52:11 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.3">
+<tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.4">
   <description> - tabulate variable sites from BAM datasets</description>
   <requirements>
-    <requirement type="package" version="0.0.3">nvc</requirement>
+    <requirement type="package" version="0.0.4">nvc</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" />
@@ -103,7 +103,7 @@
     <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
     <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with possible alternate alleles"/>
     
-    <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
+    <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="True" label="Report counts by strand"/>
     
     <conditional name="advanced_options">
         <param name="advanced_options_selector" type="select" label="Show Advanced Options">
@@ -145,6 +145,21 @@
           <param name="coverage_dtype" value="uint8" />
           <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
       </test>
+      <test>
+          <param name="reference_source_selector" value="history" />
+          <param name="input_bam" value="fake_phiX174_reads_1.bam" ftype="bam" />
+          <param name="ref_file" value="phiX174.fasta" ftype="fasta" />
+          <param name="regions" value="0" />
+          <param name="min_support_depth" value="0" />
+          <param name="min_base_quality" value="" />
+          <param name="min_mapping_quality" value="" />
+          <param name="ploidy" value="2" />
+          <param name="variants_only" value="False" />
+          <param name="use_strand" value="True" />
+          <param name="advanced_options_selector" value="advanced" />
+          <param name="coverage_dtype" value="uint8" />
+          <output name="output_vcf" file="fake_phiX174_reads_1_test_out_2.vcf" compare="contains" />
+      </test>
   </tests>
   <help>
 The **Naive Variant Caller** tool (NVC).