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comparison artic_minion.xml @ 0:c411e2205442 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
author iuc
date Thu, 30 Apr 2020 04:05:09 -0400
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children 20165d3a8fb1
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1 <tool id="artic_minion" name="ARTIC minion" version="1.1.0_rc2+galaxy0">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="1.1.0_rc2">artic</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 mkdir -p 'scheme/name/version' &&
8 #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":
9 ln -s '${primer_scheme_source.primer_scheme_bedfile.fields.path}' 'scheme/name/version/name.scheme.bed' &&
10 #else:
11 ln -s '${primer_scheme_source.primer_scheme_bedfile}' 'scheme/name/version/name.scheme.bed' &&
12 #end if
13 #if str( $reference_source.reference_source_selector ) == "history":
14 ln -s '${reference_source.reference}' 'scheme/name/version/name.reference.fasta' &&
15 samtools faidx 'scheme/name/version/name.reference.fasta' &&
16 #else:
17 ln -s '${reference_source.reference.fields.path}' 'scheme/name/version/name.reference.fasta' &&
18 samtools faidx 'scheme/name/version/name.reference.fasta' &&
19 #end if
20 artic minion
21 --threads \${GALAXY_SLOTS:-1}
22 --normalise '${normalise}'
23 --read-file '${read_file}'
24 --scheme-directory 'scheme'
25 --medaka
26 $bwa
27 'name/version'
28 '${read_file.element_identifier}'
29 ]]></command>
30 <inputs>
31 <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
32 <param argument="--normalise" type="integer" min="1" value="200" max="2000" label="Coverage normalisation depth"/>
33 <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/>
34 <conditional name="primer_scheme_source">
35 <param name="primer_scheme_source_selector" type="select" label="Select a primer scheme from your history or use one from a tool data table?"
36 help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table">
37 <option value="tool_data_table">From tool data table</option>
38 <option value="history">From history</option>
39 </param>
40 <when value="tool_data_table">
41 <param name="primer_scheme_bedfile" type="select" format="bed" label="Primer Scheme">
42 <options from_data_table="primer_scheme_bedfiles">
43 <validator type="no_options" message="No primer scheme .bed files are available" />
44 </options>
45 </param>
46 </when>
47 <when value="history">
48 <param name="primer_scheme_bedfile" type="data" format="bed" label="Primer Scheme" />
49 </when>
50 </conditional>
51 <conditional name="reference_source">
52 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in reference?" >
53 <option value="cached">Use a built-in reference</option>
54 <option value="history">Use a reference from history</option>
55 </param>
56 <when value="cached">
57 <param name="reference" type="select" label="Using reference genome" help="Select genome from the list">
58 <options from_data_table="all_fasta">
59 <filter type="sort_by" column="2" />
60 <validator type="no_options" message="No references are available" />
61 </options>
62 </param>
63 </when>
64 <when value="history">
65 <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence"
66 help="You can upload a FASTA sequence to the history and use it as reference" />
67 </when>
68 </conditional>
69 </inputs>
70 <outputs>
71 <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="${tool.name} on ${on_string}: trimmed alignment" />
72 <data name="variants_tabular" format="tabular" from_work_dir="*.variants.tab" label="${tool.name} on ${on_string}: variants table" />
73 <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: variants vcf" />
74 <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" />
75 </outputs>
76 <tests>
77 <test>
78 <param name="reference_source_selector" value="history" />
79 <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" />
80 <param name="reference" value="nCoV-2019.reference.fasta" />
81 <param name="primer_scheme_source_selector" value="tool_data_table" />
82 <param name="primer_scheme_bedfile" value="test_entry" />
83 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" />
84 </test>
85 <test>
86 <param name="reference_source_selector" value="history" />
87 <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" />
88 <param name="reference" value="nCoV-2019.reference.fasta" />
89 <param name="primer_scheme_source_selector" value="history" />
90 <param name="primer_scheme_bedfile" value="nCoV-2019.V1.bed" />
91 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" />
92 </test>
93 <test>
94 <param name="reference_source_selector" value="tool_data_table" />
95 <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" />
96 <param name="reference" value="test_entry" />
97 <param name="primer_scheme_source_selector" value="tool_data_table" />
98 <param name="primer_scheme_bedfile" value="test_entry" />
99 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" />
100 </test>
101 </tests>
102 <help><![CDATA[
103 This tool aligns MinION reads that were generated from a tiling amplicon library against a viral reference sequence.
104 It generates a consensus fasta file and a vcf variant file.
105
106 This tool is configured to use the experimental 'medaka' variant caller.
107 ]]></help>
108 <citations>
109 </citations>
110 </tool>