Mercurial > repos > devteam > picard
comparison picard_CollectWgsMetrics.xml @ 14:486d7500da69 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
author | iuc |
---|---|
date | Mon, 16 Apr 2018 21:27:09 -0400 |
parents | 41b8d087a2d2 |
children | a5a13ea16d17 |
comparison
equal
deleted
inserted
replaced
13:c7dd8d7946b8 | 14:486d7500da69 |
---|---|
1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.0"> | 1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
2 <description>compute metrics for evaluating of whole genome sequencing experiments</description> | 2 <description>compute metrics for evaluating of whole genome sequencing experiments</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 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
8 @java_options@ | 9 @java_options@ |
9 @symlink_element_identifier@ | 10 @symlink_element_identifier@ |
10 ##set up input files | 11 ##set up input files |
11 | 12 |
12 #set $reference_fasta_filename = "localref.fa" | 13 #set $reference_fasta_filename = "localref.fa" |
13 | 14 |
14 #if str( $reference_source.reference_source_selector ) == "history": | 15 @handle_reference_source@ |
15 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
16 #else: | |
17 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
18 #end if | |
19 | 16 |
20 picard | 17 picard |
21 CollectWgsMetrics | 18 CollectWgsMetrics |
22 INPUT='$escaped_element_identifier' | 19 INPUT='$escaped_element_identifier' |
23 OUTPUT="${outFile}" | 20 OUTPUT="${outFile}" |
98 Default value: 250. | 95 Default value: 250. |
99 | 96 |
100 @more_info@ | 97 @more_info@ |
101 | 98 |
102 </help> | 99 </help> |
100 <expand macro="citations" /> | |
103 </tool> | 101 </tool> |
104 | |
105 |