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comparison tools/mentalist_call/mentalist_call.xml @ 0:1d9e3950ce61 draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
author dfornika
date Wed, 20 Dec 2017 17:36:03 -0500
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-1:000000000000 0:1d9e3950ce61
1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.3">
2 <requirements>
3 <requirement type="package" version="0.1.3">mentalist</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 mentalist
7 call
8 -o '$output_file'
9 --db '$kmer_db.fields.path'
10 #if $input_type.sPaired == "paired":
11 -s $input_type.pInput1.name $input_type.pInput1 $input_type.pInput2
12 #elif $input_type.sPaired == "collections":
13 -s $input_type.fastq_collection.name $input_type.fastq_collection.forward $input_type.fastq_collection.reverse
14 #end if
15 ]]></command>
16 <inputs>
17 <conditional name="input_type">
18 <param name="sPaired" type="select" label="Single Pair or Collection">
19 <option value="collections">Paired-end Collections</option>
20 <option value="paired">Paired-end</option>
21 </param>
22 <when value="paired">
23 <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
24 <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
25 </when>
26 <when value="collections">
27 <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" />
28 </when>
29 </conditional>
30 <param name="kmer_db" type="select">
31 <options from_data_table="mentalist_databases">
32 <validator type="no_options" message="No MentaLiST databases are available" />
33 </options>
34 </param>
35 </inputs>
36 <outputs>
37 <data name="output_file" format="tabular"/>
38 </outputs>
39 <help><![CDATA[
40 ]]></help>
41 <citations>
42 <citation type="doi">10.1101/172858</citation>
43 </citations>
44 </tool>