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comparison sniffles.xml @ 3:09f5c6f3088a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
author iuc
date Thu, 26 Sep 2024 11:44:13 +0000
parents 3f6f028f418f
children 43fffeed243f
comparison
equal deleted inserted replaced
2:220316da739c 3:09f5c6f3088a
14 </version_command> 14 </version_command>
15 <command detect_errors="exit_code"> 15 <command detect_errors="exit_code">
16 <![CDATA[ 16 <![CDATA[
17 ln -f -s '${input}' input.bam && 17 ln -f -s '${input}' input.bam &&
18 ln -f -s '${input.metadata.bam_index}' input.bam.bai && 18 ln -f -s '${input.metadata.bam_index}' input.bam.bai &&
19 #if $reference_genome.genome_type_select != "None":
20 #if $reference_genome.genome_type_select == "indexed":
21 ln -f -s '${reference_genome.genome.fields.path}' 'reference.fa' &&
22 #else:
23 ln -f -s '${reference_genome.genome}' 'reference.fa' &&
24 #end if
25 #end if
19 sniffles 26 sniffles
20 -t \${GALAXY_SLOTS:-2} 27 -t \${GALAXY_SLOTS:-2}
21 -i 'input.bam' 28 -i 'input.bam'
22 -v '$output' 29 -v '$output'
23 ## must set allow-overwrite since the new output vcf file exists 30 ## must set allow-overwrite since the new output vcf file exists
24 --allow-overwrite 31 --allow-overwrite
25 #if $reference_genome.genome_type_select != "None": 32 #if $reference_genome.genome_type_select != "None":
26 #if $reference_genome.genome_type_select == "indexed": 33 --reference 'reference.fa'
27 --reference '${reference_genome.genome.fields.path}'
28 #else:
29 --reference '${reference_genome.genome}'
30 #end if
31 #end if 34 #end if
32 ## general_options 35 ## general_options
33 --minsupport '$general_options.minsupport' 36 --minsupport '$general_options.minsupport'
34 --max-splits-kb '$general_options.maxsplitskb' 37 --max-splits-kb '$general_options.maxsplitskb'
35 --minsvlen '$general_options.minsvlen' 38 --minsvlen '$general_options.minsvlen'
107 <test> <!-- test 5 - Advanced - mosaic --> 110 <test> <!-- test 5 - Advanced - mosaic -->
108 <param name="input" value="reads_region.bam"/> 111 <param name="input" value="reads_region.bam"/>
109 <param name="mosaic" value="--mosaic"/> 112 <param name="mosaic" value="--mosaic"/>
110 <output name="output" file="expected_outcome5.vcf" lines_diff="4"/> 113 <output name="output" file="expected_outcome5.vcf" lines_diff="4"/>
111 </test> 114 </test>
115 <test> <!-- test 6 - reference -->
116 <param name="input" value="reads_region.bam"/>
117 <conditional name="reference_genome">
118 <param name="genome_type_select" value="history"/>
119 <param name="genome" value="humsamp.fa"/>
120 <param name="genome.ext" value="fasta"/>
121 </conditional>
122 <output name="output" file="expected_outcome6.vcf" lines_diff="4"/>
123 </test>
112 </tests> 124 </tests>
113 <help> 125 <help>
114 <![CDATA[ 126 <![CDATA[
115 ######## 127 ########
116 Sniffles 128 Sniffles