Mercurial > repos > iuc > lorikeet_spoligotype
comparison lorikeet.xml @ 1:f9c37d0b3002 draft
planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352
author | iuc |
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date | Tue, 19 Jun 2018 02:01:02 -0400 |
parents | d35cc8e07d00 |
children | da22667725c7 |
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0:d35cc8e07d00 | 1:f9c37d0b3002 |
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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> |