Mercurial > repos > dereeper > vcftools_filter_stats_diversity

changeset 1:aad8f697f86b draft

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planemo upload commit 305985afd3b7c3d47f531149c2f1a279af2d12aa
author dereeper
date Thu, 19 Apr 2018 12:17:15 -0400
parents 7130bd0d2a83
children 67c96d03fc3f
files VCFToolsFilter/vcfToolsFilter.xml VCFToolsSlidingWindow/vcfToolsSlidingWindow.xml VCFToolsStats/vcfToolsStats.xml
diffstat 3 files changed, 12 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/VCFToolsFilter/vcfToolsFilter.xml	Mon Apr 16 08:57:13 2018 -0400
+++ b/VCFToolsFilter/vcfToolsFilter.xml	Thu Apr 19 12:17:15 2018 -0400
@@ -6,8 +6,9 @@
     <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
     <requirements>
         <requirement type="binary">perl</requirement>
+	<requirement type="package" version="1.6.924">perl-bioperl</requirement>
 	<requirement type="package" version="0.1.14">vcftools</requirement>
-	<requirement type="package" version="1.6.924">perl-bioperl</requirement>
+        <requirement type="package" version="0.1.14">perl-vcftools-vcf</requirement>
     </requirements>
     
     <code file="find_indiv.py"/>
@@ -16,6 +17,9 @@
     <stdio>
         <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
         <exit_code range="1:" level="fatal" />
+        <regex match="No such file or directory"
+           level="fatal"
+           description="Failed to install vcftools package" />
     </stdio>    
 
     <!-- [REQUIRED] The command to execute -->
--- a/VCFToolsSlidingWindow/vcfToolsSlidingWindow.xml	Mon Apr 16 08:57:13 2018 -0400
+++ b/VCFToolsSlidingWindow/vcfToolsSlidingWindow.xml	Thu Apr 19 12:17:15 2018 -0400
@@ -9,16 +9,17 @@
         <requirement type="package" version="1.6.924">perl-bioperl</requirement>
 	<requirement type="package" version="0.1.14">vcftools</requirement>
 	<requirement type="package" version="0.1.14">perl-vcftools-vcf</requirement>
-
     </requirements>
     
     <!-- [STRONGLY RECOMMANDED] Exit code rules -->
     <stdio>
         <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
         <exit_code range="1:" level="fatal" />
+        <regex match="No such file or directory"
+           level="fatal"
+           description="Failed to install vcftools package" />
     </stdio>
     
-    
     <!-- [REQUIRED] The command to execute -->
     <command interpreter="bash">
     	vcfToolsSlidingWindow.sh ${filein} $window $filelog ${fileout_taj} ${fileout_tstv} ${fileout_windowed} ${fileout_snp} 
--- a/VCFToolsStats/vcfToolsStats.xml	Mon Apr 16 08:57:13 2018 -0400
+++ b/VCFToolsStats/vcfToolsStats.xml	Thu Apr 19 12:17:15 2018 -0400
@@ -8,12 +8,16 @@
         <requirement type="binary">perl</requirement>
 	<requirement type="package" version="1.6.924">perl-bioperl</requirement>
 	<requirement type="package" version="0.1.14">vcftools</requirement>
+        <requirement type="package" version="0.1.14">perl-vcftools-vcf</requirement>
     </requirements>
     
     <!-- [STRONGLY RECOMMANDED] Exit code rules -->
     <stdio>
         <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
         <exit_code range="1:" level="fatal" />
+        <regex match="No such file or directory"
+           level="fatal"
+           description="Failed to install vcftools package" />
     </stdio>
     
     <!-- [REQUIRED] The command to execute -->