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comparison tb_profiler_profile.xml @ 0:8529c9fd63ad draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
author iuc
date Tue, 02 Apr 2019 09:03:16 -0400
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children 5182e1a99313
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1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.1.0">
2 <description>Infer strain types and drug resistance markers from sequences</description>
3 <requirements>
4 <requirement type="package" version="2.1.0">tb-profiler</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 tb-profiler profile
8
9 --platform '${platform.value}'
10
11 #if $fastq_or_bam.input_select.value == "fastq":
12 --read1 '${read1}'
13
14 #if $read2:
15 --read2 '${read2}'
16 #end if
17
18 #else if $fastq_or_bam.input_select.value == "bam":
19 --bam '${bam_input}'
20 #end if
21
22 --call_method '${call_method}'
23 --min_depth '${min_depth}'
24 --threads "\${GALAXY_SLOTS:-1}"
25 --mapper '${mapper}'
26 --min_gene_frac '${min_gene_frac}'
27
28 #if $txt:
29 --txt
30 #end if
31
32 ]]></command>
33 <inputs>
34 <param name="platform" type="select" label="Platform">
35 <option value="Illumina" selected="true">Illumina</option>
36 <option value="minION">minION</option>
37 </param>
38 <conditional name="fastq_or_bam">
39 <param name="input_select" type="select" label="Input File Type">
40 <option value="fastq">fastq</option>
41 <option value="bam">bam</option>
42 </param>
43 <when value="fastq">
44 <param name="read1" type="data" format="fastq" label="Read1" help="First read file (default: None)"/>
45 <param name="read2" type="data" format="fastq" optional="true" label="Read2" help="Second read file (default: None)"/>
46 </when>
47 <when value="bam">
48 <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/>
49 </when>
50 </conditional>
51 <param name="call_method" type="select" label="Call Method" help="Level of quality stringency required. (default: low)">
52 <option value="low" selected="true">low</option>
53 <option value="high">high</option>
54 <option value="optimise">optimise</option>
55 </param>
56 <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
57 <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
58 <option value="bwa" selected="true">bwa</option>
59 <option value="minimap2">minimap2</option>
60 <option value="bowtie2">bowtie2</option>
61 </param>
62 <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)"/>
63 <param name="txt" label="Generate text file ouput" type="boolean" value="false" help="Create reader-friendly text output in addition to standard JSON output (default: False)"/>
64 </inputs>
65 <outputs>
66 <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
67 <data name="results_txt" format="txt" from_work_dir="results/tbprofiler.results.txt" label="${tool.name} on ${on_string}: Results.txt">
68 <filter>txt</filter>
69 </data>
70 </outputs>
71 <tests>
72 <test expect_num_outputs="1">
73 <param name="read1" value="rif_resistant.fastq.gz"/>
74 <output name="results_json" value="results_1.json"/>
75 </test>
76 <test expect_num_outputs="2">
77 <param name="read1" value="rif_resistant.fastq.gz"/>
78 <param name="txt" value="true"/>
79 <param name="call_method" value="high"/>
80 <param name="min_depth" value="11"/>
81 <output name="results_json" value="results_2.json"/>
82 <output name="results_txt" value="results_2.txt"/>
83 </test>
84 </tests>
85 <help><![CDATA[
86 Summary
87 =======
88
89 The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using SAMtools. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).
90
91 Produces a JSON output file by default.
92
93 ]]></help>
94 <citations>
95 <citation type="bibtex">
96 @UNPUBLISHED{Phelan2016,
97 author = {Phelan, Jody},
98 title = {TBProfiler},
99 year = {2016},
100 url = {https://github.com/jodyphelan/TBProfiler},
101 }
102 </citation>
103 </citations>
104 </tool>