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1 <tool id="make_nr" name="Make FASTA non-redundant" version="0.0.1">
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2 <description>by combining duplicated sequences</description>
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3 <requirements>
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4 <requirement type="package" version="1.67">biopython</requirement>
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5 </requirements>
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6 <version_command>
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7 python $__tool_directory__/make_nr.py --version
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8 </version_command>
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9 <command detect_errors="aggressive">
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10 python $__tool_directory__/make_nr.py $alphasort -s '$separator' -o '$output'
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11 #for $f in $input
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12 '$f'
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13 #end for
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14 </command>
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15 <inputs>
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16 <param name="input" type="data" format="fasta,fasta.gz" multiple="True"
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17 label="Input FASTA sequence file(s)"/>
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18 <param argument="separator" type="text" size="10" area="False" value=";"
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19 label="Separator string to use when combining the identifiers of duplicate sequences"
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20 help="A single character is recommended, e.g. the semi-colon, or comma">
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21 <sanitizer>
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22 <valid initial="default">
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23 <add value=";"/>
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24 <add value="|"/>
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25 </valid>
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26 </sanitizer>
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27 </param>
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28 <param argument="alphasort" type="select" label="Treatment of identifiers when combining duplicates with the separator">
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29 <option value="">Use the order they appear in the input file(s)</option>
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30 <option value="-a">Sort alphabetically before combining them</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data name="output" format="fasta" label="$on_string (NR)" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input" value="duplicates.fasta" ftype="fasta"/>
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39 <output name="output" file="duplicates.nr.fasta" ftype="fasta"/>
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40 </test>
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41 <test>
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42 <param name="input" value="duplicates.fasta.gz" ftype="fasta.gz"/>
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43 <output name="output" file="duplicates.nr.fasta" ftype="fasta"/>
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44 </test>
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45 <test>
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46 <param name="input" value="more_duplicates.fasta,duplicates.fasta" ftype="fasta"/>
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47 <output name="output" file="deduplicate.nosortids.fasta" ftype="fasta"/>
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48 </test>
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49 <test>
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50 <param name="input" value="more_duplicates.fasta,duplicates.fasta" ftype="fasta"/>
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51 <param name="alphasort" value="-a"/>
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52 <output name="output" file="deduplicate.sortids.fasta" ftype="fasta"/>
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53 </test>
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54 </tests>
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55 <help>
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56 **What it does**
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57
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58 Takes one or more input FASTA files, checks them to find any duplicate sequences
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59 (ignoring the case), and writes an output FASTA file where any duplicates appear
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60 once with combined identifier.
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61
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62 For example, using the default separator of a semi-colon::
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63
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64 >1 first entry
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65 act
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66 >2 The A-Team
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67 AAaa
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68 >3 not unique...
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69 ACgt
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70 >4
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71 CCCC
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72 >5 a duplicate
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73 acgt
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74 >6 last!
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75 GGGG
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76
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77 In this simple example ``ACGT`` appears twice (ignoring case) as entries ``3``
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78 and ``6``. Entry ``3`` is renamed as ``3;6`` and entry ``4`` is omitted::
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79
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80 >1 first entry
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81 act
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82 >2 The A-Team
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83 AAaa
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84 >3;6 representing 2 records
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85 ACgt
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86 >4
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87 CCCC
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88 >6 last!
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89 GGGG
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90
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91 This means that the representative records take the position and sequence case
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92 from the first entry with that sequence.
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93
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94 In this case the combined entry is labelled as ``3;6``, so the sort option
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95 has no effect. However, if the records appears in the file with ``6`` before
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96 ``3`` you can choose to get ``6;3`` (order from file, default) or ``3;6``
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97 (ordered alphabetically).
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98
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99 Notice the unique sequences are preserved as they were with any description
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100 or mixed case.
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101
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102
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103 **References**
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104
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105 If you cannot cite this tool directly via the GitHub URL
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106 https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr
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107 and need a traditional paper, then please cite:
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108
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109 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo (2015).
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110 NCBI BLAST+ integrated into Galaxy.
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111 *GigaScience* 4:39
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112 https://doi.org/10.1186/s13742-015-0080-7
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113
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114 This wrapper is available to install into other Galaxy Instances via the Galaxy
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115 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/make_nr
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116 </help>
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117 <citations>
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118 <citation type="doi">10.1186/1471-2105-10-421</citation>
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119 </citations>
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120 </tool>
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