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comparison picard_CollectBaseDistributionByCycle.xml @ 19:5053a18d9bc8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
author iuc
date Mon, 16 Apr 2018 21:27:29 -0400
parents 465cbb0cf2eb
children 2a17c789e0a5
comparison
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18:7615ac66c6e5 19:5053a18d9bc8
1 <tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@.0"> 1 <tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description> 2 <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">0</token>
5 </macros> 6 </macros>
6 <expand macro="requirements"> 7 <expand macro="requirements">
7 <requirement type="package" version="3.3.1">r</requirement> 8 <requirement type="package" version="3.4.1">r-base</requirement>
8 </expand> 9 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 @java_options@ 11 @java_options@
11 @symlink_element_identifier@ 12 @symlink_element_identifier@
12 ##set up input files 13 ##set up input files
13 14
14 #set $reference_fasta_filename = "localref.fa" 15 #set $reference_fasta_filename = "localref.fa"
15 16
16 #if str( $reference_source.reference_source_selector ) == "history": 17 @handle_reference_source@
17 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
18 #else:
19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
20 #end if
21 18
22 picard 19 picard
23 CollectBaseDistributionByCycle 20 CollectBaseDistributionByCycle
24 INPUT='$escaped_element_identifier' 21 INPUT='$escaped_element_identifier'
25 OUTPUT="${outFile}" 22 OUTPUT="${outFile}"
105 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default 102 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
106 103
107 @more_info@ 104 @more_info@
108 105
109 </help> 106 </help>
107 <expand macro="citations" />
110 </tool> 108 </tool>
111
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