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comparison uvp.xml @ 0:76eefba8e661 draft

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"planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/uvp commit 2482e856a9414983c82d94c9f59ff8985574895e-dirty"
author dfornika
date Fri, 11 Oct 2019 18:24:47 -0400
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children 845a20f1fa5e
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-1:000000000000 0:76eefba8e661
1 <tool id="uvp" name="Unified Variant analysis Pipeline for M. tuberculosis complex" version="@TOOL_VERSION@+galaxy0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">uvp</requirement>
8 </requirements>
9 <version_command>uvp --version</version_command>
10 <command detect_errors="exit_code">
11 <![CDATA[
12 uvp
13 --threads \${GALAXY_SLOTS:-1}
14 #if $single_paired.single_paired_selector == 'yes'
15 -n '${single_paired.forward_input.element_identifier}'
16 -q '${single_paired.forward_input}'
17 -q2 '${single_paired.reverse_input}'
18 #elif $single_paired.single_paired_selector == "collection":
19 -n '${single_paired.input_pair.forward.element_identifier}'
20 -q '${single_paired.input_pair.forward}'
21 -q2 '${single_paired.input_pair.reverse}'
22 #else:
23 -n '${single_paired.input_sequences.element_identifier}'
24 -q '${single_paired.input_sequences}'
25 #end if
26 --krakendb '${kraken_database.fields.path}'
27 -r '${reference}'
28 ${annotate}
29 --outdir outdir
30 ]]>
31 </command>
32 <inputs>
33 <conditional name="single_paired">
34 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
35 <option value="collection">Collection</option>
36 <option value="yes">Paired</option>
37 <option selected="True" value="no">Single</option>
38 </param>
39 <when value="collection">
40 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
41 </when>
42 <when value="yes">
43 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
44 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
45 </when>
46 <when value="no">
47 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
48 </when>
49 </conditional>
50 <param name="kraken_database" type="select">
51 <options from_data_table="kraken_databases">
52 <validator type="no_options" message="No Kraken databases are available" />
53 </options>
54 </param>
55 <param name="reference" type="data" format="fasta" label="Reference Sequence" />
56 <param name="annotate" type="boolean" truevalue="--annotate" falsevalue="" />
57 </inputs>
58 <outputs>
59 <data name="low_quals" label="Low-quality" format="tabular" from_work_dir="outdir/QC/low_quals.txt"/>
60 </outputs>
61 <tests>
62 </tests>
63 <help>
64 <![CDATA[
65 ]]>
66 </help>
67 <expand macro="citations" />
68 </tool>