Mercurial > repos > iuc > bcftools_convert_to_vcf

diff bcftools_convert_to_vcf.xml @ 7:367ba501b6eb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 16:05:01 -0500
parents 7b50ab23976c
children 843e008b15fd
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--- a/bcftools_convert_to_vcf.xml	Tue Dec 12 14:02:26 2017 -0500
+++ b/bcftools_convert_to_vcf.xml	Thu Feb 21 16:05:01 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@VERSION@">
+<tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@TOOL_VERSION@">
     <description>Converts other formats to VCF/BCFk</description>
     <macros>
         <token name="@EXECUTABLE@">convert</token>
@@ -70,7 +70,7 @@
                 <expand macro="macro_columns"/>
             </when>
             <when value="gvcf">
-                <param name="input_file" type="data" format="gvcf" label="Genomic VCF (GATK HaplotypeCaller)" />
+                <param name="input_file" type="data" format="vcf" label="Genomic VCF (GATK HaplotypeCaller)" />
                 <expand macro="macro_fasta_ref" />
             </when>
             <when value="gen_sample">
@@ -139,7 +139,7 @@
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" />
-                    <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tEND=20;BLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" />
+                    <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" />
                 </assert_contents>
             </output>
         </test>