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