Mercurial > repos > iuc > bcftools_convert_to_vcf

diff bcftools_convert_to_vcf.xml @ 5:6911c0cb6b7d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
author iuc
date Thu, 13 Apr 2017 16:21:34 -0400
parents dccf11c79157
children 45d35a05dbaa
line wrap: on
line diff
--- a/bcftools_convert_to_vcf.xml	Sat Mar 11 17:50:51 2017 -0500
+++ b/bcftools_convert_to_vcf.xml	Thu Apr 13 16:21:34 2017 -0400
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.3.1">samtools</requirement>
+        <expand macro="samtools_requirement"/>
     </expand>
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[
@@ -15,16 +15,16 @@
 #if $convert.convert_from == 'gvcf':
   #set $input_vcf = 'input.vcf.gz'
   #if $convert.input_file.is_of_type('vcf')
-    bgzip -c "$convert.input_file" > $input_vcf &&
+    bgzip -c '$convert.input_file' > $input_vcf &&
     bcftools index $input_vcf &&
   #elif $convert.input_file.is_of_type('vcf_bgzip')
-    ln -s "$convert.input_file" $input_vcf
+    ln -s '$convert.input_file' $input_vcf
   #elif $convert.input_file.is_of_type('bcf')
     #set $input_vcf = 'input.bcf'
-    ln -s "$convert.input_file" $input_vcf &&
+    ln -s '$convert.input_file' $input_vcf &&
     bcftools index $input_vcf &&
   #elif $convert.input_file.is_of_type('bcf_bgzip')
-    ln -s "$convert.input_file" $input_vcf &&
+    ln -s '$convert.input_file' $input_vcf &&
   #end if
 #end if
 #set $section = $convert
@@ -36,11 +36,11 @@
 
 #set $section = $convert
 #if $convert.convert_from == 'gen_sample':
-  --gensample2vcf "$convert.input_file,$convert.input_sample"
+  --gensample2vcf '$convert.input_file,$convert.input_sample'
 #elif $convert.convert_from == 'hap_sample':
-  --hapsample2vcf "$convert.input_file,$convert.input_sample"
+  --hapsample2vcf '$convert.input_file,$convert.input_sample'
 #elif $convert.convert_from == 'hap_legend_sample':
-  --haplegendsample2vcf "$convert.input_file,$convert.input_legend,$convert.input_sample"
+  --haplegendsample2vcf '$convert.input_file,$convert.input_legend,$convert.input_sample'
 #elif $convert.convert_from == 'gvcf':
    @FASTA_REF@
    --gvcf2vcf $input_vcf
@@ -48,9 +48,9 @@
    @FASTA_REF@
    @SAMPLES@
    @COLUMNS@
-   --tsv2vcf "$convert.input_file"
+   --tsv2vcf '$convert.input_file'
 #end if
-> "$output_file"
+> '$output_file'
 ]]>
     </command>
     <inputs>