Mercurial > repos > jjohnson > arriba

comparison arriba.xml @ 12:73fd7703a743 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit fe2e3c7429c5bea23690a27b5889b502984ad58a"
author jjohnson
date Tue, 26 Apr 2022 20:35:35 +0000
parents 8ed8af5836d1
children 1d459aaa5765
comparison
equal deleted inserted replaced
11:8ed8af5836d1 12:73fd7703a743
11 </macros> 11 </macros>
12 <expand macro="requirements" /> 12 <expand macro="requirements" />
13 <expand macro="version_command" /> 13 <expand macro="version_command" />
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 @GENOME_SOURCE@ 15 @GENOME_SOURCE@
16 #if $blacklist
17 #if $blacklist.is_of_type('tabular.gz')
18 #set $blacklist_file = 'blacklist.tsv.gz'
19 ln -sf '$blacklist' $blacklist_file &&
20 #else
21 #set $blacklist_file = $blacklist
22 #end if
23 #end if
24 #if $known_fusions
25 #if $known_fusions.is_of_type('tabular.gz')
26 #set $known_fusions_file = 'known_fusions.tsv.gz'
27 ln -sf '$known_fusions' $known_fusions_file &&
28 #else
29 #set $known_fusions_file = $known_fusions
30 #end if
31 #end if
32 #if $tags
33 #if $tags.is_of_type('tabular.gz')
34 #set $tags_file = 'tags.tsv.gz'
35 ln -sf '$tags' $tags_file &&
36 #else
37 #set $tags_file = $tags
38 #end if
39 #end if
16 #if str($input_params.input_source) == "use_fastq" 40 #if str($input_params.input_source) == "use_fastq"
17 #set $readFilesCommand = '' 41 #set $readFilesCommand = ''
18 #set $read2 = '' 42 #set $read2 = ''
19 #if str($input_params.singlePaired.sPaired) == 'paired_collection': 43 #if str($input_params.singlePaired.sPaired) == 'paired_collection':
20 #if $input_params.singlePaired.input.forward.is_of_type('fastq.gz', 'fastqsanger.gz'): 44 #if $input_params.singlePaired.input.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
42 #end if 66 #end if
43 #if str($input_params.index.index_source) == "history" 67 #if str($input_params.index.index_source) == "history"
44 #set $star_index_dir = $input_params.index.star_index.extra_files_path 68 #set $star_index_dir = $input_params.index.star_index.extra_files_path
45 #else 69 #else
46 #set $star_index_dir = $input_params.index.arriba_ref.fields.star_index 70 #set $star_index_dir = $input_params.index.arriba_ref.fields.star_index
47 #end if
48 #if $blacklist
49 #if $blacklist.is_of_type('tabular.gz')
50 #set $blacklist_file = 'blacklist.tsv.gz'
51 ln -sf '$blacklist' $blacklist_file &&
52 #else
53 #set $blacklist_file = $blacklist
54 #end if
55 #end if
56 #if $known_fusions
57 #if $known_fusions.is_of_type('tabular.gz')
58 #set $known_fusions_file = 'known_fusions.tsv.gz'
59 ln -sf '$known_fusions' $known_fusions_file &&
60 #else
61 #set $known_fusions_file = $known_fusions
62 #end if
63 #end if
64 #if $tags
65 #if $tags.is_of_type('tabular.gz')
66 #set $tags_file = 'tags.tsv.gz'
67 ln -sf '$tags' $tags_file &&
68 #else
69 #set $tags_file = $tags
70 #end if
71 #end if 71 #end if
72 72
73 STAR 73 STAR
74 --runThreadN \${GALAXY_SLOTS:-1} 74 --runThreadN \${GALAXY_SLOTS:-1}
75 --genomeDir $star_index_dir 75 --genomeDir $star_index_dir