Mercurial > repos > iuc > lorikeet_spoligotype

comparison lorikeet.xml @ 1:f9c37d0b3002 draft

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planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
author iuc
date Tue, 19 Jun 2018 02:01:02 -0400
parents d35cc8e07d00
children da22667725c7
comparison
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0:d35cc8e07d00 1:f9c37d0b3002
1 <tool id="lorikeet_spoligotype" name="lorikeet spoligotyping" version="@TOOL_VERSION@+galaxy0" profile="17.01"> 1 <tool id="lorikeet_spoligotype" name="lorikeet spoligotyping" version="@TOOL_VERSION@+galaxy0" profile="17.01">
2 <description>M. tuberculosis DNA fingerprinting</description> 2 <description>M. tuberculosis DNA fingerprinting</description>
3 3
4 <macros> 4 <macros>
5 <token name="@TOOL_VERSION@">17</token> 5 <token name="@TOOL_VERSION@">20</token>
6 </macros> 6 </macros>
7 7
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">lorikeet</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">lorikeet</requirement>
10 </requirements> 10 </requirements>
19 -s '${spacer_source.spacer}' 19 -s '${spacer_source.spacer}'
20 #end if 20 #end if
21 ]]> 21 ]]>
22 </command> 22 </command>
23 <inputs> 23 <inputs>
24 <param name="input" label="Input sequences" type="data" format="bam" help="Reads of sample(s) being spoligotyped" /> 24 <param name="input" label="Input sequences" type="data" format="bam,fastq,fastq.gz" help="Reads of sample(s) being spoligotyped" />
25 <conditional name="spacer_source"> 25 <conditional name="spacer_source">
26 <param type="select" name="source_type" label="Source for spacer sequences"> 26 <param type="select" name="source_type" label="Source for spacer sequences">
27 <option selected="true" value="builtin">Built-in</option> 27 <option selected="true" value="builtin">Built-in</option>
28 <option value="file">File with custom spacers</option> 28 <option value="file">File with custom spacers</option>
29 </param> 29 </param>
38 <data name="output_txt" format="txt" label="Spoligotype on ${on_string}" /> 38 <data name="output_txt" format="txt" label="Spoligotype on ${on_string}" />
39 </outputs> 39 </outputs>
40 <tests> 40 <tests>
41 <test> 41 <test>
42 <param name="input" value="input.bam" ftype="bam" /> 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.fastq" ftype="fastq" />
51 <output name="output_txt">
52 <assert_contents>
53 <has_text text="1111111111 1111111011 1111111111 1100001111 111" />
54 </assert_contents>
55 </output>
56 </test>
57 <test>
58 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
43 <output name="output_txt"> 59 <output name="output_txt">
44 <assert_contents> 60 <assert_contents>
45 <has_text text="1111111111 1111111011 1111111111 1100001111 111" /> 61 <has_text text="1111111111 1111111011 1111111111 1100001111 111" />
46 </assert_contents> 62 </assert_contents>
47 </output> 63 </output>