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comparison picard_SamToFastq.xml @ 2:9227b8c3093b

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Updated command line format per dev team standards.
author devteam <devteam@galaxyproject.org>
date Tue, 02 Apr 2013 09:42:36 -0400
parents 1cd7f3b42609
children 3d4f1fa26f0e
comparison
equal deleted inserted replaced
1:e0232cbac965 2:9227b8c3093b
6 -p ' 6 -p '
7 java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC 7 java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
8 -jar "\$JAVA_JAR_PATH/SamToFastq.jar" 8 -jar "\$JAVA_JAR_PATH/SamToFastq.jar"
9 INPUT="${input_sam}" 9 INPUT="${input_sam}"
10 VALIDATION_STRINGENCY="LENIENT" 10 VALIDATION_STRINGENCY="LENIENT"
11 RE_REVERSE=${re_reverse} 11 RE_REVERSE="${re_reverse}"
12 INCLUDE_NON_PF_READS=${include_non_pf_reads} 12 INCLUDE_NON_PF_READS="${include_non_pf_reads}"
13 #if str( $clipping_attribute ): 13 #if str( $clipping_attribute ):
14 CLIPPING_ATTRIBUTE="${clipping_attribute}" 14 CLIPPING_ATTRIBUTE="${clipping_attribute}"
15 #end if 15 #end if
16 #if str( $clipping_action ): 16 #if str( $clipping_action ):
17 CLIPPING_ACTION="${clipping_action}" 17 CLIPPING_ACTION="${clipping_action}"
20 READ1_TRIM="${read1_trim}" 20 READ1_TRIM="${read1_trim}"
21 #end if 21 #end if
22 #if str( $read1_max_bases_to_write ): 22 #if str( $read1_max_bases_to_write ):
23 READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}" 23 READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
24 #end if 24 #end if
25 INCLUDE_NON_PRIMARY_ALIGNMENTS=${include_non_primary_alignments} 25 INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"
26 26
27 #if str( $output_per_read_group_selector ) == 'per_sam_file': 27 #if str( $output_per_read_group_selector ) == 'per_sam_file':
28 ##OUTPUT_PER_RG=false 28 ##OUTPUT_PER_RG=false
29 FASTQ="${output_fastq1}" 29 FASTQ="${output_fastq1}"
30 30
52 READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}" 52 READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}"
53 #end if 53 #end if
54 #end if 54 #end if
55 ' 55 '
56 --read_group_file_1 "${output_fastq1}" 56 --read_group_file_1 "${output_fastq1}"
57 --new_files_path "${$__new_file_path__}" 57 --new_files_path "${__new_file_path__}"
58 --file_id_1 "${output_fastq1.id}" 58 --file_id_1 "${output_fastq1.id}"
59 #end if 59 #end if
60 </command> 60 </command>
61 <inputs> 61 <inputs>
62 <param name="input_sam" type="data" format="sam,bam" label="BAM/SAM file" /> 62 <param name="input_sam" type="data" format="sam,bam" label="BAM/SAM file" />