diff freebayes.xml @ 29:156b60c1530f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b

--- a/freebayes.xml	Tue Jun 06 18:41:18 2017 -0400
+++ b/freebayes.xml	Wed Oct 25 08:29:45 2017 -0400
@@ -1,11 +1,11 @@
-<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-1">
+<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-0">
     <description>bayesian genetic variant detector</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="4.1.3">gawk</requirement>
-        <requirement type="package" version="20160622">parallel</requirement>
+        <requirement type="package" version="20170422">parallel</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
     ##set up input files
@@ -614,7 +614,7 @@
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="simple"/>
-            <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
+            <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -623,7 +623,7 @@
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="naive_w_filters"/>
             <param name="min_coverage" value="14"/>
-            <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
+            <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -632,7 +632,7 @@
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="naive_w_filters"/>
             <param name="min_coverage" value="14"/>
-            <output name="output_vcf" file="freebayes-phix174-test3.vcf" compare="contains"/>
+            <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" />
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -642,7 +642,7 @@
             <param name="options_type_selector" value="full"/>
             <param name="population_model_selector" value="set"/>
             <param name="P" value="1"/>
-            <output name="output_vcf" file="freebayes-phix174-test4.vcf" compare="contains"/>
+            <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
         </test>
     </tests>
     <help>
@@ -685,5 +685,20 @@
 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
 TNG was developed by Bjoern Gruening.
     </help>
-    <expand macro="citations" />
+    <expand macro="citations">
+        <citation type="bibtex">
+            @article{Tange2011a,
+                title = {GNU Parallel - The Command-Line Power Tool},
+                author = {O. Tange},
+                address = {Frederiksberg, Denmark},
+                journal = {;login: The USENIX Magazine},
+                month = {Feb},
+                number = {1},
+                volume = {36},
+                url = {http://www.gnu.org/s/parallel},
+                year = {2011},
+                pages = {42-47}
+            }
+        </citation>
+    </expand>
 </tool>