Mercurial > repos > iuc > bcftools_plugin_counts

comparison 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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4:902fd5bfb7f6 5:5bae20e2d7c8
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 @PREPARE_ENV@ 12 @PREPARE_ENV@
13 @PREPARE_INPUT_FILE@ 13 @PREPARE_INPUT_FILE@
14 #set $section = $sec_restrict 14 #set $section = $sec_restrict
15 @PREPARE_TARGETS_FILE@ 15 @PREPARE_TARGETS_FILE@
16 @PREPARE_REGIONS_FILE@
17
16 bcftools plugin @EXECUTABLE@ 18 bcftools plugin @EXECUTABLE@
17 19
18 ## VCF input section 20 ## VCF input section
19 #set $section = $sec_restrict 21 #set $section = $sec_restrict
20 @INCLUDE@ 22 @INCLUDE@
22 @REGIONS@ 24 @REGIONS@
23 @TARGETS@ 25 @TARGETS@
24 26
25 ## Primary Input/Outputs 27 ## Primary Input/Outputs
26 @INPUT_FILE@ | tee counts_file.txt 28 @INPUT_FILE@ | tee counts_file.txt
27 && sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > "$output_file" 29 && sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > '$output_file'
28 ]]> 30 ]]>
29 </command> 31 </command>
30 <configfiles> 32 <configfiles>
31 <configfile name="transform"><![CDATA[ 33 <configfile name="transform"><![CDATA[
32 from __future__ import print_function 34 from __future__ import print_function