Mercurial > repos > iuc > mykrobe_predict
comparison macro.xml @ 3:e8405163fb4e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
author | iuc |
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date | Tue, 10 Aug 2021 11:29:58 +0000 |
parents | cedd631dc124 |
children | a2e3ad69ee23 |
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2:cedd631dc124 | 3:e8405163fb4e |
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1 <?xml version="1.1"?> | 1 <?xml version="1.1"?> |
2 <macros> | 2 <macros> |
3 <token name="@TOOL_VERSION@">0.10.0</token> | |
3 <xml name="requirements"> | 4 <xml name="requirements"> |
4 <requirements> | 5 <requirements> |
5 <requirement type="package" version="0.7.0">mykrobe</requirement> | 6 <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement> |
6 </requirements> | 7 </requirements> |
7 </xml> | 8 </xml> |
8 <token name="@select_inputs@"> | 9 <token name="@select_inputs@"> |
9 <![CDATA[ | 10 <![CDATA[ |
10 #set $name='sample' | 11 #set $name='sample' |
11 #set $type='fastq' | |
12 ## Adding sample name, indicate specie and inputs fastq(s) files | |
13 #if $data_type.type == "paired": | |
14 | |
15 ln -s '$data_type.fastq_input1' sample_1.fastq && | |
16 ln -s '$data_type.fastq_input2' sample_2.fastq && | |
17 | |
18 | |
19 #elif $data_type.type == "collection": | |
20 #set $name=str($data_type.fastq_input1.name) | |
21 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq && | |
22 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq && | |
23 | |
24 #elif $data_type.type == "single": | |
25 | |
26 | |
27 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): | |
28 ln -s '$data_type.fastq_input1' sample.fastq && | |
29 | |
30 #end if | |
31 | |
32 #if $data_type.fastq_input1.is_of_type('bam'): | |
33 ln -s '$data_type.fastq_input1' sample.bam && | |
34 #set $type='bam' | |
35 #end if | |
36 | |
37 #end if | |
38 ]]> | 12 ]]> |
39 </token> | 13 </token> |
40 | 14 |
41 <token name="@shared_options@"> | 15 <token name="@shared_options@"> |
42 <![CDATA[ | 16 <![CDATA[ |
95 <option value="single">Single-end Data</option> | 69 <option value="single">Single-end Data</option> |
96 <option value="paired">Paired-end Data</option> | 70 <option value="paired">Paired-end Data</option> |
97 <option value="collection">Collection Paired-end Data</option> | 71 <option value="collection">Collection Paired-end Data</option> |
98 </param> | 72 </param> |
99 <when value="single"> | 73 <when value="single"> |
100 <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/> | 74 <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/> |
101 </when> | 75 </when> |
102 <when value="paired"> | 76 <when value="paired"> |
103 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/> | 77 <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/> |
104 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/> | 78 <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/> |
105 </when> | 79 </when> |
106 <when value="collection"> | 80 <when value="collection"> |
107 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" /> | 81 <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" /> |
108 </when> | 82 </when> |
109 </conditional> | 83 </conditional> |
110 </xml> | 84 </xml> |
111 | 85 |
112 <xml name="options"> | 86 <xml name="options"> |