Mercurial > repos > iuc > mykrobe_predict

annotate macro.xml @ 0:32f8ee6a4712 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
author iuc
date Sat, 13 Jan 2018 09:01:13 -0500
parents
children 9b5743b8208f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
2 <macros>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
3 <xml name="requirements">
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
4 <requirements>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
5 <requirement type="package" version="0.5.6">mykrobe</requirement>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
6 </requirements>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
7 </xml>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
8
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
9 <token name="@select_inputs@">
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
10 <![CDATA[
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
11 #set $name='sample'
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
12 #set $type='fastq'
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
13 ## Adding sample name, indicate specie and inputs fastq(s) files
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
14 #if $data_type.type == "paired":
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
15
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
16 ln -s '$data_type.fastq_input1' sample_1.fastq &&
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
17 ln -s '$data_type.fastq_input2' sample_2.fastq &&
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
18
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
19
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
20 #elif $data_type.type == "collection":
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
21 #set $name=str($data_type.fastq_input1.name)
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
22 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq &&
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
23 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq &&
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
24
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
25 #elif $data_type.type == "single":
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
26
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
27
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
28 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
29 ln -s '$data_type.fastq_input1' sample.fastq &&
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
30
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
31 #end if
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
32
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
33 #if $data_type.fastq_input1.is_of_type('bam'):
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
34 ln -s '$data_type.fastq_input1' sample.bam &&
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
35 #set $type='bam'
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
36 #end if
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
37
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
38 #end if
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
39 ]]>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
40 </token>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
41
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
42 <xml name="inputs">
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
43 <conditional name="data_type">
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
44 <param name="type" type="select" label="Specify the read type.">
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
45 <option value="single">Single-end Data</option>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
46 <option value="paired">Paired-end Data</option>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
47 <option value="collection">Collection Paired-end Data</option>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
48 </param>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
49 <when value="single">
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
50 <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
51 </when>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
52 <when value="paired">
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
53 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
54 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
55 </when>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
56 <when value="collection">
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
57 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
58 </when>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
59 </conditional>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
60 </xml>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
61
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
62 <token name="@ATTRIBUTION@">
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
63 <![CDATA[
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
64
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
65 **MyKrobe predict - Antibiotic resistance predictions**
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
66
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
67 Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
68 using Bruijn graph.
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
69 ]]>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
70 </token>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
71
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
72 <xml name="citation">
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
73 <citations>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
74 <citation type="doi">10.1038/ncomms10063</citation>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
75 </citations>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
76 </xml>
32f8ee6a4712 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
77 </macros>