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comparison bbmap.xml @ 0:2b64db8ec69e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
author iuc
date Mon, 04 Oct 2021 12:13:52 +0000
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children 7bc91654244d
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-1:000000000000 0:2b64db8ec69e
1 <tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>short-read aligner</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 #import os
9 #import re
10
11 #if str($ref_source_cond.ref_source) == 'cached'
12 #set ref = str($ref_source_cond.reference.fields.path)
13 #else:
14 #set ref = $ref_source_cond.reference
15 #end if
16
17 #if str($input_type_cond.input_type) in ['single', 'pair']:
18 #set read1 = $input_type_cond.read1
19 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
20 ## bbmap uses the file extension to determine the input format.
21 #set ext = $read1_identifier + '.fastq'
22 #if $read1.ext.endswith('.gz'):
23 #set ext = $ext + '.gz'
24 #end if
25 #set read1_file = $read1_identifier + $ext
26 ln -s '${read1}' '${read1_file}' &&
27 #if str($input_type_cond.input_type) == 'pair':
28 #set read2 = $input_type_cond.read2
29 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
30 #set read2_file = $read2_identifier + $ext
31 ln -s '${read2}' '${read2_file}' &&
32 #end if
33 #else:
34 #set read1 = $input_type_cond.reads_collection['forward']
35 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
36 ## bbmap uses the file extension to determine the input format.
37 #set ext = $read1_identifier + '.fastq'
38 #if $read1.ext.endswith('.gz'):
39 #set ext = $ext + '.gz'
40 #end if
41 #set read1_file = $read1_identifier + $ext
42 ln -s '${read1}' '${read1_file}' &&
43 #set read2 = $input_type_cond.reads_collection['reverse']
44 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name))
45 #set read2_file = $read2_identifier + $ext
46 ln -s '${read2}' '${read2_file}' &&
47 #end if
48
49 bbmap.sh t=\${GALAXY_SLOTS:-4} ref='${ref}'
50 #if str($input_type_cond.input_type) == 'single':
51 in='${read1_file}'
52 #else:
53 in1='${read1_file}' in2='${read2_file}'
54 #end if
55 #if str($output_sort) == 'coordinate':
56 out='mapped.bam'; samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output' 'mapped.bam'
57 #elif str($output_sort) == 'name':
58 out='mapped.bam'; samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output' 'mapped.bam'
59 #else:
60 out='mapped.bam' && mv 'mapped.bam' '$output'
61 #end if
62 ]]></command>
63 <inputs>
64 <conditional name="input_type_cond">
65 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
66 <option value="single" selected="true">Single dataset</option>
67 <option value="pair">Dataset pair</option>
68 <option value="paired">List of dataset pairs</option>
69 </param>
70 <when value="single">
71 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
72 </when>
73 <when value="pair">
74 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
75 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
76 </when>
77 <when value="paired">
78 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
79 </when>
80 </conditional>
81 <expand macro="reference_source_cond"/>
82 <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can significantly extend the run time of the tool (it runs using a single thread).">
83 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
84 <option value="name">Sort by read names</option>
85 <option value="unsorted">Not sorted (sorted as input)</option>
86 </param>
87 </inputs>
88 <outputs>
89 <data format="bam" name="output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
90 <expand macro="dbKeyActionsBBMap"/>
91 <change_format>
92 <when input="output_sort" value="name" format="qname_sorted.bam" />
93 <when input="output_sort" value="unsorted" format="qname_input_sorted.bam" />
94 </change_format>
95 </data>
96 </outputs>
97 <tests>
98 <!-- Single file, cached reference, output coordinate sorted -->
99 <test expect_num_outputs="1">
100 <param name="input_type" value="single"/>
101 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
102 <output name="output" file="output1.bam" ftype="bam" lines_diff="4">
103 <metadata name="dbkey" value="89" />
104 </output>
105 </test>
106 <!-- Paired reads in separate datasets, cached reference, output name sorted -->
107 <test expect_num_outputs="1">
108 <param name="input_type" value="pair"/>
109 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
110 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
111 <param name="output_sort" value="name"/>
112 <output name="output" file="output2.bam" ftype="qname_sorted.bam" lines_diff="4">
113 <metadata name="dbkey" value="89" />
114 </output>
115 </test>
116 <!-- Collection of Paired reads, history reference, output unsorted -->
117 <test expect_num_outputs="1">
118 <param name="input_type" value="paired"/>
119 <param name="reads_collection">
120 <collection type="paired">
121 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
122 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
123 </collection>
124 </param>
125 <param name="ref_source" value="history"/>
126 <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/>
127 <param name="output_sort" value="unsorted"/>
128 <output name="output" file="output3.bam" ftype="qname_input_sorted.bam" lines_diff="4">
129 <metadata name="dbkey" value="89" />
130 </output>
131 </test>
132 </tests>
133 <help>
134 **What it does**
135
136 BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. It is fast and extremely accurate, particularly
137 with highly mutated genomes or reads with long indels, even whole-gene deletions over 100kbp long. It has no upper limit
138 to genome size or number of contigs and has been successfully used for mapping to an 85 gigabase soil metagenome with over
139 200 million contigs. the indexing phase is very fast compared to other aligners.
140
141 BBMap can output many different statistics files; an empirical read quality histogram, insert-size distribution, and genome
142 coverage with or without generating a sam file. It is useful in quality control of libraries and sequencing runs or
143 evaluating new sequencing platforms.
144
145 **Options**
146
147 *Bam sorting mode* - the generated bam files can be sorted according to three criteria: coordinates, names and input order.
148
149 * Sort by chromosomal coordinates - the file is sorted by coordinates (i.e., the reads from the beginning of the first
150 chromosome are first in the file.
151 * Sort by read names - the file is sorted by the reference ID (i.e., the QNAME field).
152 * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file.
153
154 </help>
155 <expand macro="citations"/>
156 </tool>
157