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comparison bio_hansel.xml @ 2:09ebaa5192ab draft

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planemo upload for repository https://github.com/phac-nml/bio_hansel commit d5a37b4f48178ee8179883d0f6cf550824e975f0
author nml
date Fri, 27 Oct 2017 12:40:00 -0400
parents ba271365095e
children 29faaa849e41
comparison
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1:ba271365095e 2:09ebaa5192ab
1 <tool id="bio_hansel" name="Salmonella Subtyping" version="0.1.2"> 1 <tool id="bio_hansel" name="Salmonella Subtyping" version="0.1.3">
2 <description>Genome assemblies and/or whole-genome sequencing readset</description> 2 <description>Genome assemblies and/or whole-genome sequencing readset</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.0">bio_hansel</requirement> 4 <requirement type="package" version="0.1.0">bio_hansel</requirement>
5 <requirement type="package" version="17.2.0">attrs</requirement> 5 <requirement type="package" version="17.2.0">attrs</requirement>
6 </requirements> 6 </requirements>
11 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' && 11 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' &&
12 ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name' && 12 ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name' &&
13 13
14 #elif $data_type.type == "collection": 14 #elif $data_type.type == "collection":
15 15
16 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.forward.name' && 16 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1 &&
17 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.reverse.name' && 17 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2 &&
18 18
19 #elif $data_type.type == "single": 19 #elif $data_type.type == "single":
20 20
21 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): 21 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
22 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' && 22 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' &&
68 68
69 #if $data_type.type == "single": 69 #if $data_type.type == "single":
70 '$data_type.fastq_input1.name' 70 '$data_type.fastq_input1.name'
71 71
72 #elif $data_type.type =="collection": 72 #elif $data_type.type =="collection":
73 -p '$data_type.fastq_input1.forward.name' '$data_type.fastq_input1.reverse.name' 73 -p '$data_type.fastq_input1.name'_1 '$data_type.fastq_input1.name'_2
74 74
75 #elif $data_type.type =="paired": 75 #elif $data_type.type =="paired":
76 -p '$data_type.fastq_input1.name' '$data_type.fastq_input2.name' 76 -p '$data_type.fastq_input1.name' '$data_type.fastq_input2.name'
77 77
78 #end if 78 #end if