Mercurial > repos > iuc > pbmm2
comparison pbmm2.xml @ 0:29eec6c7bab2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 commit b9fe99d8335825c6c23f569034354323b794127a
author | iuc |
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date | Wed, 08 Mar 2023 12:00:46 +0000 |
parents | |
children | 55b7b257e12f |
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1 <tool id="pbmm2" name="pbmm2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
2 <description>map PacBio reads to a reference genome.</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="xrefs"/> | |
7 <expand macro="requirements"/> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 ## set up files | |
10 #set reads_fn = 'reads.' + $reads.ext | |
11 ln -s '$reads' '$reads_fn' && | |
12 | |
13 #if $reference_source.reference_source_selector == 'history': | |
14 #set ref_fn = 'reference.fa' | |
15 ln -f -s '$reference_source.ref_file' '$ref_fn' && | |
16 #else: | |
17 #set ref_fn = $reference_source.ref_file.fields.path | |
18 #end if | |
19 | |
20 ## run pbmm2 | |
21 pbmm2 align | |
22 -j \${GALAXY_SLOTS:-4} | |
23 '$reads_fn' | |
24 '$ref_fn' | |
25 out.aligned.bam | |
26 --sort | |
27 ]]></command> | |
28 <inputs> | |
29 <!-- from tools-iuc minimap2 wrapper --> | |
30 <conditional name="reference_source"> | |
31 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?"> | |
32 <option value="cached">Use a built-in genome index</option> | |
33 <option value="history">Use a genome from history and build index</option> | |
34 </param> | |
35 <when value="cached"> | |
36 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> | |
37 <options from_data_table="all_fasta"> | |
38 <filter type="sort_by" column="2" /> | |
39 <validator type="no_options" message="No reference genomes are available" /> | |
40 </options> | |
41 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
42 </param> | |
43 </when> | |
44 <when value="history"> | |
45 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> | |
46 </when> | |
47 </conditional> | |
48 <param type="data" name="reads" format="fastq,fastq.gz,fasta,fasta.gz,bam" label="reads" help="PacBio reads in BAM or [gzipped] fasta or fastq format." /> | |
49 </inputs> | |
50 <outputs> | |
51 <data name="bam" format="bam" from_work_dir="out.aligned.bam" label="${tool.name} on ${on_string} (BAM file)" /> | |
52 </outputs> | |
53 <tests> | |
54 <!-- test1: basic test --> | |
55 <test expect_num_outputs="1"> | |
56 <param name="reference_source_selector" value="history" /> | |
57 <param name="ref_file" ftype="fasta" value="bnd-ref.fasta"/> | |
58 <param name="reads" value="bnd.bam"/> | |
59 <output name="bam"> | |
60 <assert_contents> | |
61 <has_size value="2778" delta="200" /> | |
62 </assert_contents> | |
63 </output> | |
64 </test> | |
65 <!-- test2: map some reads for use with pbgcpp --> | |
66 <test expect_num_outputs="1"> | |
67 <param name="reference_source_selector" value="history" /> | |
68 <param name="ref_file" ftype="fasta" value="All4mer.V2.01_Insert.fa"/> | |
69 <param name="reads" value="out.aligned_subreads.bam"/> | |
70 <output name="bam"> | |
71 <assert_contents> | |
72 <has_size value="539464" delta="50000" /> | |
73 </assert_contents> | |
74 </output> | |
75 </test> | |
76 <!-- test3: cached genome --> | |
77 <test> | |
78 <param name="reference_source_selector" value="cached" /> | |
79 <param name="ref_file" value="bnd-ref"/> | |
80 <param name="reads" value="bnd.bam"/> | |
81 <output name="bam"> | |
82 <assert_contents> | |
83 <has_size value="2778" delta="200" /> | |
84 </assert_contents> | |
85 </output> | |
86 </test> | |
87 </tests> | |
88 <help><![CDATA[ | |
89 **What it does** | |
90 | |
91 A minimap2 wrapper for PacBio data: native PacBio data in ⇨ native | |
92 PacBio BAM out. | |
93 | |
94 -------------- | |
95 | |
96 pbmm2 is Pacific Biosciences’ wrapper for | |
97 `minimap2 <https://github.com/lh3/minimap2>`__\ ’s C API. It supports | |
98 native PacBio input. Output can be used directly for polishing using | |
99 `pbgcpp <root?tool_id=pbgcpp>`__. | |
100 | |
101 **Input**: PacBio reads in bam or [gzipped] fasta or fastq format. | |
102 **NOTE**: to use the output of pbmm2 for pbgcpp (GenomicConsensus), you | |
103 have to provide PacBio CLR reads in bam format. You can use pbmm2 to | |
104 align other types of PacBio reads in [gzipped] fasta or fastq format, | |
105 but you can’t use the output for pbgcpp (GenomicConsensus). | |
106 | |
107 **Output**: A **sorted** PacBio BAM file, suitable for use with | |
108 pbgcpp (previously known as GenomicConsensus). | |
109 | |
110 ]]></help> | |
111 <expand macro="creator"/> | |
112 </tool> |