Mercurial > repos > iuc > mykrobe_predict

comparison macro.xml @ 3:0f2f9e53b6fa draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
author iuc
date Tue, 10 Aug 2021 11:29:03 +0000
parents 8782fc7296b2
children 70a3a5377e6d
comparison
equal deleted inserted replaced
2:8782fc7296b2 3:0f2f9e53b6fa
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">