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5
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1 <tool id="PHYLO_filter" name="Filter and trim" version="1.2.0">
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2
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2 <description>sequences</description>
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6
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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2
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6 <requirements>
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7 <requirement type="package">yapp_env</requirement>
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8 </requirements>
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6
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9 <stdio>
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10 <expand macro="basic_errors"/>
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11 </stdio>
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2
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12 <version_command>seqmagick --version</version_command>
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13 <command interpreter="bash">
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14 filter-wrapper.sh ${config}
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15 </command>
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16 <inputs>
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17 <!-- TODO: can take either fasta+qual or fastq -->
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18 <param name="plate_id" type="integer" value="1" label="Plate number"/>
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19 <param name="zone_id" type="integer" value="1" label="Zone number"/>
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20 <param name="raw_seqs" type="data" format="fasta" label="Unfiltered sequences"/>
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21 <param name="input_qual" type="data" format="qual" label="Sequence quality data"/>
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22 <!-- TODO: handle MID format for multi-sample sequencing; see http://qiime.org/scripts/split_libraries.html -->
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23 <param name="barcodes" type="data" format="csv" label="Barcodes"/>
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24 <param name="primer" type="text" label="Primer" value="GCGGACTACCVGGGTATCTAAT" area="True" size="1x40"/>
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25 <param name="min_length" type="integer" min="100" max="1000" value="350" label="Minimum sequence length"/>
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26 <param name="min_quality" type="integer" min="0" max="63" value="35" label="Minimum mean sequence quality"/>
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27 <param name="reverse_complement" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Reads uniformly correspond to negative strands"/>
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28 </inputs>
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29 <outputs>
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30 <data name="filtered_seqs" format="fasta" label="Filtered sequences"/>
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31 <data name="filter_report" format="tabular" label="Filtering report"/>
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32 <data name="filter_details" format="data" label="Filtering details"/>
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33 <data name="split_map" format="csv" label="Read-to-specimen map"/>
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5
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34 <data name="seq_qual_report" format="html" label="Sequence quality report"/>
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2
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35 </outputs>
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36 <configfiles>
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5
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37 <configfile name="plate_json">
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38 {
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39 "plate": ${plate_id},
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40 "name": "Plate ${plate_id}",
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41 "zones": [
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42 {
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43 "zone": ${zone_id},
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44 "cleaning_stats": "${filter_details}"
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45 }
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46 ]
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47 }
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48 </configfile>
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2
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49 <configfile name="config">
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50 RAW_SEQS="${raw_seqs}"
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51 INPUT_QUAL="${input_qual}"
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52 BARCODES="${barcodes}"
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53 PRIMER="${primer}"
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54 MIN_LENGTH="${min_length}"
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55 MIN_QUALITY="${min_quality}"
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56 REVERSE_COMPLEMENT="${reverse_complement}"
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5
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57 PLATE_JSON="${plate_json}"
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2
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58
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59 FILTERED_SEQS="${filtered_seqs}"
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60 FILTER_REPORT="${filter_report}"
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61 FILTER_DETAILS="${filter_details}"
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62 SPLIT_MAP="${split_map}"
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5
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63 SQR="${seq_qual_report}"
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64 SQR_DIR="${seq_qual_report.files_path}"
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2
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65 </configfile>
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66 </configfiles>
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67 <!-- The contents of the help tag is parsed as reStructuredText. Please see
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68 help-template.rst for examples of commonly-used sections in other Galaxy
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69 tools. -->
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70 <help>
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71
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72 .. class:: infomark
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73
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74 **What it does**
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75
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76 This tool truncates and removes sequences that don’t match a set of quality
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77 criteria, as well as mapping sequence barcodes to specimens. It takes input
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78 sequences in FASTA format and a quality file, and outputs the filtered
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5
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79 sequences as well as a filtering summary and a sequence quality report.
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2
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80
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81 The default quality filter settings are:
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82
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83 +---------------------------+------+
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84 |parameter |value |
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85 +===========================+======+
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86 |--min-length |350 |
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87 +---------------------------+------+
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88 |--min-mean-quality |35 |
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89 +---------------------------+------+
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90 |--quality-window |30 |
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91 +---------------------------+------+
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92 |--quality-window-prop |0.9 |
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93 +---------------------------+------+
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94 |--quality-window-mean-qual |15 |
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95 +---------------------------+------+
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96
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97 See seqmagick's `quality filter documentation`_ for full explanations of these
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98 parameters.
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99
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100 .. _quality filter documentation: http://fhcrc.github.io/seqmagick/quality_filter.html
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101
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102 </help>
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6
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103 <citations>
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104 <expand macro="cite_seqmagick"/>
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105 <expand macro="cite_biopython"/>
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106 </citations>
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2
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107 </tool>
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