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comparison star_fusion.xml @ 3:137942fac417 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
author iuc
date Mon, 06 Jan 2020 11:08:46 -0500
parents 0b44456754e2
children
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equal deleted inserted replaced
2:04b73d626680 3:137942fac417
1 <tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3" profile="17.01"> 1 <tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3+galaxy1" profile="17.01">
2 <description>detect fusion genes in RNA-Seq data</description> 2 <description>detect fusion genes in RNA-Seq data</description>
3 <requirements> 3 <requirements>
4 <!-- Bio-conda -->
5 <requirement type="package" version="0.5.4">star-fusion</requirement> 4 <requirement type="package" version="0.5.4">star-fusion</requirement>
6 </requirements> 5 </requirements>
7 6
8 <stdio> 7 <stdio>
9 <regex match="command not found" source="stderr" level="fatal"/> 8 <regex match="command not found" source="stderr" level="fatal"/>
24 </stdio> 23 </stdio>
25 24
26 <version_command>STAR-Fusion --version 2>&amp;1 | grep version | grep -o -E "software version.*?"</version_command> 25 <version_command>STAR-Fusion --version 2>&amp;1 | grep version | grep -o -E "software version.*?"</version_command>
27 26
28 <command><![CDATA[ 27 <command><![CDATA[
29 ## 1. ensure the blastn file is provided as *.gz 28 ## 1. ensure the blastn file is provided as *.gz
30 if file --mime-type '${blast_pairs}' | grep -q /gzip\$; then 29 gzip -1 -c -- '${blast_pairs}' > blast_pairs.gz &&
31 gzip_suffix='' ; 30
32 else 31 ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory
33 ## Older versions of gzip do not support the -k option to keep 32 ## - @todo once write a decent STAR and STAR Fusion data manager
34 ## the original file - this should be an universion solution 33 prep_genome_lib.pl
35 34 --genome_fa '${fasta_type.ownFile}'
36 gzip -1 -c -- '${blast_pairs}' > '${blast_pairs}.gz' && 35 --gtf '${geneModel}'
37 gzip_suffix='.gz' ; 36 --blast_pairs blast_pairs.gz
38 fi && 37 --CPU \${GALAXY_SLOTS:-1}
39 38 --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
40 ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory 39 &&
41 ## - @todo once write a decent STAR and STAR Fusion data manager 40
42 prep_genome_lib.pl 41 ## Link in fastq files so they have appropriate extensions
43 --genome_fa '${fasta_type.ownFile}' 42 #if str($input_params.input_source) != "use_chimeric":
44 --gtf '${geneModel}' 43 #if $input_params.left_fq.is_of_type("fastq.gz"):
45 --blast_pairs "${blast_pairs}\$gzip_suffix" 44 #set read1 = 'input_1.fastq.gz'
46 --CPU \${GALAXY_SLOTS:-1} 45 #else:
47 --output_dir "\$(pwd)/tmp_star_fusion_genome_dir" 46 #set read1 = 'input_1.fastq'
48 && 47 #end if
49 48 ln -f -s '${input_params.left_fq}' ${read1} &&
50 ## Link in fastq files so they have appropriate extensions 49
51 #if str($input_params.input_source) != "use_chimeric": 50 #if $input_params.right_fq:
52 #if $input_params.left_fq.is_of_type("fastq.gz"): 51 #if $input_params.right_fq.is_of_type("fastq.gz"):
53 #set read1 = 'input_1.fastq.gz' 52 #set read2 = 'input_2.fastq.gz'
54 #else: 53 #else:
55 #set read1 = 'input_1.fastq' 54 #set read2 = 'input_2.fastq'
56 #end if
57 ln -f -s '${input_params.left_fq}' ${read1} &&
58
59 #if $input_params.right_fq:
60 #if $input_params.right_fq.is_of_type("fastq.gz"):
61 #set read2 = 'input_2.fastq.gz'
62 #else:
63 #set read2 = 'input_2.fastq'
64 #end if
65 ln -f -s '${input_params.right_fq}' ${read2} &&
66 #end if
67 #end if 55 #end if
68 56 ln -f -s '${input_params.right_fq}' ${read2} &&
69 ## 3. Run STAR-Fusion 57 #end if
70 STAR-Fusion 58 #end if
71 #if str($input_params.input_source) == "use_chimeric": 59
72 --chimeric_junction '${input_params.chimeric_junction}' 60 ## 3. Run STAR-Fusion
73 #else: 61 STAR-Fusion
74 --left_fq ${read1} 62 #if str($input_params.input_source) == "use_chimeric":
75 #if $input_params.right_fq: 63 --chimeric_junction '${input_params.chimeric_junction}'
76 --right_fq ${read2} 64 #else:
77 #end if 65 --left_fq ${read1}
78 #end if 66 #if $input_params.right_fq:
79 67 --right_fq ${read2}
80 --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir"
81
82 #if str($params.settingsType) == "full":
83 --min_junction_reads $params.min_junction_reads
84 --min_sum_frags $params.min_sum_frags
85 --max_promiscuity $params.max_promiscuity
86 --min_novel_junction_support $params.min_novel_junction_support
87 --min_alt_pct_junction $params.min_alt_pct_junction
88 --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist
89 --E $params.E
90 #end if 68 #end if
69 #end if
70
71 --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir"
72
73 #if str($params.settingsType) == "full":
74 --min_junction_reads $params.min_junction_reads
75 --min_sum_frags $params.min_sum_frags
76 --max_promiscuity $params.max_promiscuity
77 --min_novel_junction_support $params.min_novel_junction_support
78 --min_alt_pct_junction $params.min_alt_pct_junction
79 --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist
80 --E $params.E
81 #end if
91 ]]></command> 82 ]]></command>
92 83
93 <inputs> 84 <inputs>
94 <conditional name="input_params"> 85 <conditional name="input_params">
95 <param name="input_source" 86 <param name="input_source"