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comparison lorikeet.xml @ 0:d35cc8e07d00 draft

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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
author iuc
date Tue, 08 May 2018 04:23:01 -0400
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1 <tool id="lorikeet_spoligotype" name="lorikeet spoligotyping" version="@TOOL_VERSION@+galaxy0" profile="17.01">
2 <description>M. tuberculosis DNA fingerprinting</description>
3
4 <macros>
5 <token name="@TOOL_VERSION@">17</token>
6 </macros>
7
8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">lorikeet</requirement>
10 </requirements>
11
12 <command detect_errors="exit_code"><![CDATA[
13 #set $input_file = 'input.' + $input.extension
14 ln -s '${input}' $input_file &&
15 lorikeet spoligotype
16 -o '${output_txt}'
17 $input_file
18 #if $spacer_source.source_type == 'file':
19 -s '${spacer_source.spacer}'
20 #end if
21 ]]>
22 </command>
23 <inputs>
24 <param name="input" label="Input sequences" type="data" format="bam" help="Reads of sample(s) being spoligotyped" />
25 <conditional name="spacer_source">
26 <param type="select" name="source_type" label="Source for spacer sequences">
27 <option selected="true" value="builtin">Built-in</option>
28 <option value="file">File with custom spacers</option>
29 </param>
30 <when value="builtin">
31 </when>
32 <when value="file">
33 <param argument="--spacer" type="data" format="fasta" label="Spacer file" help="FASTA format file containing customer spacer library" />
34 </when>
35 </conditional>
36 </inputs>
37 <outputs>
38 <data name="output_txt" format="txt" label="Spoligotype on ${on_string}" />
39 </outputs>
40 <tests>
41 <test>
42 <param name="input" value="input.bam" ftype="bam" />
43 <output name="output_txt">
44 <assert_contents>
45 <has_text text="1111111111 1111111011 1111111111 1100001111 111" />
46 </assert_contents>
47 </output>
48 </test>
49 <test>
50 <param name="input" value="input.bam" ftype="bam" />
51 <param name="source_type" value="file" />
52 <param name="spacer" value="custom_spacers.fasta" ftype="fasta" />
53 <output name="output_txt">
54 <assert_contents>
55 <has_text text="1111111111 0000000000 0000000000 0000000000 000" />
56 </assert_contents>
57 </output>
58 </test>
59 </tests>
60 <help><![CDATA[
61 Lorikeet_ is a tool for digital spoligotyping_ of M. tuberculosis strains
62 from Illumina data. Input is a file of Illumina reads and output is
63 a spoligotyping report.
64
65 While by default lorikeet uses its own built-in collection of spacer
66 sequences, a custom file of spacers can be provided if necessary.
67
68 .. _Lorikeet: https://github.com/AbeelLab/lorikeet
69 .. _spoligotyping: https://link.springer.com/protocol/10.1007%2F978-1-60327-999-4_10
70 ]]>
71 </help>
72 <citations>
73 <citation type="doi">10.1371/journal.pmed.1001880</citation>
74 </citations>
75 </tool>