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comparison freyja_variants.xml @ 0:08c2d81e7942 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
author iuc
date Thu, 28 Jul 2022 09:26:32 +0000
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1 <tool id="freyja_variants" name="Freyja: Call variants"
2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
3 profile="@PROFILE@">
4 <description>
5 and get sequencing depth information
6 </description>
7 <macros>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="biotools"/>
11 <expand macro="requirements"/>
12 <expand macro="version"/>
13 <command detect_errors="exit_code"><![CDATA[
14 ln -s '$bam_file' 'bam_file' &&
15 ln -s '$ref_file' 'ref_file' &&
16 freyja variants
17 'bam_file'
18 --variants variants
19 --depths '$depths'
20 --ref 'ref_file'
21 ]]></command>
22 <inputs>
23 <param name="bam_file" type="data" format="bam" label="BAM file"
24 help="After primer trimming and alignment to reference genome."/>
25 <param name="ref_file" argument="--ref" type="data" format="fasta"
26 label="Reference sequence file"
27 help="Note that the reference should match the fasta file used for alignment."/>
28 </inputs>
29 <outputs>
30 <data name="variants" format="tabular" label="${tool.name} on ${on_string}: Variant call"
31 from_work_dir="variants.tsv">
32 </data>
33 <data name="depths" format="tabular" label="${tool.name} on ${on_string}: Sequencing depth"
34 from_work_dir="depths.tsv">
35 </data>
36 </outputs>
37 <tests>
38 <test expect_num_outputs="2">
39 <param name="bam_file" value="test.bam"/>
40 <param name="ref_file" value="NC_045512_Hu-1.fasta"/>
41 <output name="variants" ftype="tabular">
42 <assert_contents>
43 <has_text text="REF_CODON"/>
44 <has_text text="NC_045512.2"/>
45 </assert_contents>
46 </output>
47 <output name="depths" ftype="tabular">
48 <assert_contents>
49 <has_text text="NC_045512.2"/>
50 </assert_contents>
51 </output>
52 </test>
53 </tests>
54 <help><![CDATA[
55 @HELP_HEADER@
56
57 Information about **freyja variants** method
58 ============================================
59
60 The method uses both samtools and iVar.
61
62 .. class:: warningmark
63
64 Note that the reference should match the fasta file used for alignment.
65
66 Outputs
67 =======
68
69 We get both variant call and sequencing depth information with this command.
70
71 ]]></help>
72 <expand macro="citations"/>
73 </tool>