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comparison picard_ValidateSamFile.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
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equal deleted inserted replaced
12:05087b27692a 13:7e6fd3d0f16e
14 [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn` 14 [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn`
15 15
16 && 16 &&
17 17
18 ##set up input files 18 ##set up input files
19 19 @symlink_element_identifier@
20 #set $reference_fasta_filename = "localref.fa" 20 #set $reference_fasta_filename = "localref.fa"
21 21
22 #if str( $reference_source.reference_source_selector ) == "history": 22 #if str( $reference_source.reference_source_selector ) == "history":
23 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && 23 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
24 #else: 24 #else:
28 @java_options@ 28 @java_options@
29 29
30 picard 30 picard
31 ValidateSamFile 31 ValidateSamFile
32 32
33 INPUT="${inputFile}" 33 INPUT='$inputFile.element_identifier'
34 OUTPUT="${outFile}" 34 OUTPUT="${outFile}"
35 MODE="${mode}" 35 MODE="${mode}"
36 36
37 #if str( $ignore ) != "None": 37 #if str( $ignore ) != "None":
38 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd 38 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd