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comparison tools/seq_filter_by_mapping/seq_filter_by_mapping.xml @ 0:1d773da0ccf0 draft

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Uploaded v0.0.2, fixed some error messages
author peterjc
date Tue, 27 Jan 2015 08:31:13 -0500
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children 8ff0ac66f1a3
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1 <tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.2">
2 <description>from SAM/BAM file</description>
3 <requirements>
4 <requirement type="package" version="1.64">biopython</requirement>
5 <requirement type="python-module">Bio</requirement>
6 <requirement type="binary">samtools</requirement>
7 <requirement type="package" version="0.1.19">samtools</requirement>
8 </requirements>
9 <version_command interpreter="python">seq_filter_by_mapping.py --version</version_command>
10 <command interpreter="python">
11 seq_filter_by_mapping.py -i "$input_file" -f "$input_file.ext" -m $pair_mode
12 #if $output_choice_cond.output_choice=="both"
13 -p $output_pos -n $output_neg
14 #elif $output_choice_cond.output_choice=="pos"
15 -p $output_pos
16 #elif $output_choice_cond.output_choice=="neg"
17 -n $output_neg
18 #end if
19 ## Now loop over all the mapping files
20 #for i in $mapping_file#${i} #end for#
21 </command>
22 <stdio>
23 <!-- Anything other than zero is an error -->
24 <exit_code range="1:" />
25 <exit_code range=":-1" />
26 </stdio>
27 <inputs>
28 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." />
29 <param name="mapping_file" type="data" format="sam,bam" multiple="true" label="SAM/BAM mapping of those sequences" help="SAM or BAM format." />
30 <conditional name="output_choice_cond">
31 <param name="output_choice" type="select" label="Output mapped reads, unmapped reads, or both?">
32 <option value="both">Both mapped and unmapped reads, as two files</option>
33 <option value="pos">Just mapped reads, as a single file</option>
34 <option value="neg">Just unmapped reads, as a single file</option>
35 </param>
36 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
37 <when value="both" />
38 <when value="pos" />
39 <when value="neg" />
40 </conditional>
41 <param name="pair_mode" type="select" label="Paired read treatment">
42 <option value="lax" selected="true">Treat as a pair, allow either read to be mapped</option>
43 <option value="strict">Treat as a pair, require both reads to be mapped</option>
44 <!-- The following would actually be more work as have to store qname/1 and qname/2 separately for filter...
45 <option value="solo">Treat independently (will split partners when only one maps)</option>
46 -->
47 </param>
48 </inputs>
49 <outputs>
50 <data name="output_pos" format="input" metadata_source="input_file" label="$input_file.name (mapped)">
51 <filter>output_choice_cond["output_choice"] != "neg"</filter>
52 </data>
53 <data name="output_neg" format="input" metadata_source="input_file" label="$input_file.name (unmapped)">
54 <filter>output_choice_cond["output_choice"] != "pos"</filter>
55 </data>
56 </outputs>
57 <tests>
58 <test>
59 <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
60 <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" />
61 <param name="pair_mode" value="lax" />
62 <param name="output_choice" value="pos" />
63 <output name="output_pos" file="SRR639755_sample_lax.fastq" ftype="fastqsanger" />
64 </test>
65 <test>
66 <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
67 <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" />
68 <param name="pair_mode" value="strict" />
69 <param name="output_choice" value="pos" />
70 <output name="output_pos" file="SRR639755_sample_strict.fastq" ftype="fastqsanger" />
71 </test>
72 </tests>
73 <help>
74 **What it does**
75
76 By default it divides a FASTA, FASTQ or Standard Flowgram Format (SFF) file in
77 two, those sequences (or read pairs) which do or don't map in the provided
78 SAM/BAM file. You can opt to have a single output file of just the mapping reads,
79 or just the non-mapping ones.
80
81 **Example Usage**
82
83 You might wish to perform a contamination screan by mapping your reads against
84 known contaminant reference sequences, then use this tool to select only the
85 unmapped reads for further analysis (e.g. *de novo* assembly).
86
87 Similarly you might wish to map your reads against a known bacterial reference,
88 then take the non-mapping sequences forward for analysis if looking for novel
89 plasmids.
90
91
92 **References**
93
94 If you use this Galaxy tool in work leading to a scientific publication please
95 cite:
96
97 Peter J.A. Cock (2014), Galaxy tool for filtering reads by mapping
98 http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping
99
100 This tool uses Biopython to read and write SFF files, so you may also wish to
101 cite the Biopython application note (and Galaxy too of course):
102
103 Cock et al (2009). Biopython: freely available Python tools for computational
104 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
105 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
106
107 This tool is available to install into other Galaxy Instances via the Galaxy
108 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping
109 </help>
110 <citations>
111 <citation type="doi">10.1093/bioinformatics/btp163</citation>
112 </citations>
113 </tool>