Mercurial > repos > iuc > mykrobe_genotype

comparison macro.xml @ 0:d783eb846f59 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
author iuc
date Sat, 13 Jan 2018 09:02:58 -0500
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children 84f769706f7a
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-1:000000000000 0:d783eb846f59
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="0.5.6">mykrobe</requirement>
6 </requirements>
7 </xml>
8
9 <token name="@select_inputs@">
10 <![CDATA[
11 #set $name='sample'
12 #set $type='fastq'
13 ## Adding sample name, indicate specie and inputs fastq(s) files
14 #if $data_type.type == "paired":
15
16 ln -s '$data_type.fastq_input1' sample_1.fastq &&
17 ln -s '$data_type.fastq_input2' sample_2.fastq &&
18
19
20 #elif $data_type.type == "collection":
21 #set $name=str($data_type.fastq_input1.name)
22 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq &&
23 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq &&
24
25 #elif $data_type.type == "single":
26
27
28 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
29 ln -s '$data_type.fastq_input1' sample.fastq &&
30
31 #end if
32
33 #if $data_type.fastq_input1.is_of_type('bam'):
34 ln -s '$data_type.fastq_input1' sample.bam &&
35 #set $type='bam'
36 #end if
37
38 #end if
39 ]]>
40 </token>
41
42 <xml name="inputs">
43 <conditional name="data_type">
44 <param name="type" type="select" label="Specify the read type.">
45 <option value="single">Single-end Data</option>
46 <option value="paired">Paired-end Data</option>
47 <option value="collection">Collection Paired-end Data</option>
48 </param>
49 <when value="single">
50 <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/>
51 </when>
52 <when value="paired">
53 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
54 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
55 </when>
56 <when value="collection">
57 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
58 </when>
59 </conditional>
60 </xml>
61
62 <token name="@ATTRIBUTION@">
63 <![CDATA[
64
65 **MyKrobe predict - Antibiotic resistance predictions**
66
67 Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
68 using Bruijn graph.
69 ]]>
70 </token>
71
72 <xml name="citation">
73 <citations>
74 <citation type="doi">10.1038/ncomms10063</citation>
75 </citations>
76 </xml>
77 </macros>