Mercurial > repos > iuc > bcftools_plugin_counts

diff bcftools_plugin_counts.xml @ 5:5bae20e2d7c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:46:36 -0400
parents 902fd5bfb7f6
children 71c78e0eea52
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--- a/bcftools_plugin_counts.xml	Sat Mar 11 18:00:50 2017 -0500
+++ b/bcftools_plugin_counts.xml	Thu Apr 13 17:46:36 2017 -0400
@@ -13,6 +13,8 @@
 @PREPARE_INPUT_FILE@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
+@PREPARE_REGIONS_FILE@
+
 bcftools plugin @EXECUTABLE@
 
 ## VCF input section
@@ -24,7 +26,7 @@
 
 ## Primary Input/Outputs
 @INPUT_FILE@ | tee counts_file.txt  
-&& sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > "$output_file"
+&& sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > '$output_file'
 ]]>
     </command>
     <configfiles>