Mercurial > repos > iuc > bcftools_norm

comparison bcftools_norm.xml @ 5:e49eeb4059e0 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 17:42:48 -0400
parents 660f8eec689d
children 19905c025d2a
comparison
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4:660f8eec689d 5:e49eeb4059e0
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">norm</token> 5 <token name="@EXECUTABLE@">norm</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <requirement type="package" version="1.3.1">samtools</requirement> 9 <expand macro="samtools_requirement"/>
10 </expand> 10 </expand>
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@ 13 @PREPARE_ENV@
14 @PREPARE_INPUT_FILE@ 14 @PREPARE_INPUT_FILE@
15 #set $section = $sec_ref 15 #set $section = $sec_ref
16 @PREPARE_FASTA_REF@ 16 @PREPARE_FASTA_REF@
17 #set $section = $sec_restrict 17 #set $section = $sec_restrict
18 @PREPARE_TARGETS_FILE@ 18 @PREPARE_TARGETS_FILE@
19 @PREPARE_REGIONS_FILE@
19 20
20 bcftools @EXECUTABLE@ 21 bcftools @EXECUTABLE@
21 22
22 #set $section = $sec_ref 23 #set $section = $sec_ref
23 @FASTA_REF@ 24 @FASTA_REF@
50 @OUTPUT_TYPE@ 51 @OUTPUT_TYPE@
51 @THREADS@ 52 @THREADS@
52 53
53 ## Primary Input/Outputs 54 ## Primary Input/Outputs
54 @INPUT_FILE@ 55 @INPUT_FILE@
55 > "$output_file" 56 > '$output_file'
56 ]]> 57 ]]>
57 </command> 58 </command>
58 <inputs> 59 <inputs>
59 <expand macro="macro_input" /> 60 <expand macro="macro_input" />
60 <section name="sec_restrict" expanded="false" title="Restrict to"> 61 <section name="sec_restrict" expanded="false" title="Restrict to">