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comparison picard_MergeBamAlignment.xml @ 8:3a3234d7a2e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:53:10 -0400
parents 3d4f1fa26f0e
children 5eaa8a968300
comparison
equal deleted inserted replaced
7:379fdf4c41ac 8:3a3234d7a2e8
1 <tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="1.126.0"> 1 <tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.0">
2 <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> 2 <description>merge alignment data with additional info stored in an unmapped BAM dataset</description>
3 <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements>
4
5 <macros> 3 <macros>
6 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
7 </macros> 5 </macros>
8 6 <expand macro="requirements" />
9 <command> 7 <command>
10 @java_options@ 8 @java_options@
11 #set $picard_dict = "localref.dict" 9 #set $picard_dict = "localref.dict"
12 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension 10 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
13 11
40 #elif str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_two_files": 38 #elif str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_two_files":
41 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams: 39 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:
42 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}" 40 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}"
43 #end for 41 #end for
44 #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams: 42 #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams:
45 READ2_ALIGNED_BAM="${dataset.read1_aligned_bam}" 43 READ2_ALIGNED_BAM="${dataset.read2_aligned_bam}"
46 #end for 44 #end for
47 #else 45 #else
48 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams: 46 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:
49 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}" 47 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}"
50 #end for 48 #end for