Mercurial > repos > jjohnson > arriba

comparison arriba.xml @ 8:1a56888ddb7d draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit f5af83950615d8c77a3a43cf45f5ddf46000701b"
author jjohnson
date Mon, 11 Oct 2021 19:00:45 +0000
parents 25d207f7ff83
children 8c4c97fd0555
comparison
equal deleted inserted replaced
7:25d207f7ff83 8:1a56888ddb7d
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="version_command" /> 7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #if str($input_params.input_source) == "use_fastq" 9 #if str($input_params.input_source) == "use_fastq"
10 #set $readFilesCommand = ''
10 #if $input_params.left_fq.is_of_type("fastq.gz"): 11 #if $input_params.left_fq.is_of_type("fastq.gz"):
11 #set read1 = 'input_1.fastq.gz' 12 #set read1 = 'input_1.fastq.gz'
13 #set $readFilesCommand = '--readFilesCommand zcat'
12 #else: 14 #else:
13 #set read1 = 'input_1.fastq' 15 #set read1 = 'input_1.fastq'
14 #end if 16 #end if
15 ln -f -s '${input_params.left_fq}' ${read1} && 17 ln -f -s '${input_params.left_fq}' ${read1} &&
16 #if $input_params.right_fq.is_of_type("fastq.gz"): 18 #if $input_params.right_fq.is_of_type("fastq.gz"):
25 STAR 27 STAR
26 --runThreadN \${GALAXY_SLOTS:-1} 28 --runThreadN \${GALAXY_SLOTS:-1}
27 --genomeDir $star_index_dir 29 --genomeDir $star_index_dir
28 --genomeLoad NoSharedMemory 30 --genomeLoad NoSharedMemory
29 --readFilesIn $read1 $read2 31 --readFilesIn $read1 $read2
30 --readFilesCommand zcat 32 $readFilesCommand
31 --outStd BAM_Unsorted 33 --outStd BAM_Unsorted
32 --outSAMtype BAM Unsorted 34 --outSAMtype BAM Unsorted
33 --outSAMunmapped Within 35 --outSAMunmapped Within
34 --outBAMcompression 0 36 --outBAMcompression 0
35 --outFilterMultimapNmax 50 37 --outFilterMultimapNmax 50