Mercurial > repos > devteam > fastx_barcode_splitter

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author iuc
date Thu, 10 Aug 2023 06:51:23 +0000
parents da00153634dc
children
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6
8da8564e2e45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
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1 <tool id="cshl_fastx_barcode_splitter" version="1.0.1+galaxy@VERSION_SUFFIX@" profile="22.05" name="Barcode Splitter">
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2 <description></description>
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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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6 <expand macro="requirements" />
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7 <command detect_errors="aggressive"><![CDATA[
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8 mkdir split &&
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9 @CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE'
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10 --prefix 'split/'
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11 --suffix
5
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12 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
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13 '.fastqsanger'
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14 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2'):
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15 '.fastqsolexa'
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16 #elif $input.is_of_type('fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
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17 '.fastqillumina'
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18 #elif $input.is_of_type('fasta', 'fasta.gz'):
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19 '.fasta'
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20 #else:
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21 '.$input.extension'
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22 #end if
4
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23 --mismatches $mismatches
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24 --partial $partial
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25 #if $refBarcodeLocation.barcodeLocation == "idxfile":
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26 --idxfile '$refBarcodeLocation.idxfile'
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27 --idxidstrip $refBarcodeLocation.idxidstrip
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28 #else:
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29 $refBarcodeLocation.EOL
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30 #end if
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31 > '$summary'
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32 ]]></command>
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33 <inputs>
4
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34 <param name="BARCODE" type="data" format="txt" label="Barcodes to use" />
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35 <param name="input" type="data" format="@FASTAS@,@FASTQS@,fastq" label="Library to split" />
4
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36 <conditional name="refBarcodeLocation">
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37 <param name="barcodeLocation" type="select" label="Barcodes found at">
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38 <option value="bol">Start of sequence (5' end)</option>
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39 <option value="eol">End of sequence (3' end)</option>
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40 <option value="idxfile">Separate index file</option>
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41 </param>
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42 <when value="bol">
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43 <param name="EOL" type="hidden" value="--bol" />
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44 </when>
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45 <when value="eol">
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46 <param name="EOL" type="hidden" value="--eol" />
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47 </when>
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48 <when value="idxfile">
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49 <param argument="--idxidstrip" type="integer" value="1" label="Characters to strip from the end of the sequence id before matching" />
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50 <param argument="--idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
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51 </when>
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52 </conditional>
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53 <param argument="--mismatches" type="integer" value="0" label="Number of allowed mismatches" />
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54 <param argument="--partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" />
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55 </inputs>
0
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56
4
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57 <outputs>
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58 <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" />
5
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59 <collection name="split_output" type="list" label="${tool.name} on ${on_string}">
4
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60 <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" />
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61 </collection>
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62 </outputs>
0
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63
3
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64 <tests>
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65 <test>
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66 <!-- Split a FASTQ file -->
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67 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
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68 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
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69 <param name="barcodeLocation" value="bol" />
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70 <param name="mismatches" value="2" />
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71 <param name="partial" value="0" />
4
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72 <output name="summary" file="fastx_barcode_splitter1.out" />
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73 <output_collection name="split_output" type="list">
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74 <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
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75 <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
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76 <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
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77 <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
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78 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
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79 </output_collection>
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80 </test>
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81
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82 <test>
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83 <!-- Split a FASTQ.gz file -->
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84 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
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85 <param name="input" value="fastx_barcode_splitter1.fastq.gz" ftype="fastqsolexa.gz" />
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86 <param name="barcodeLocation" value="bol" />
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87 <param name="mismatches" value="2" />
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88 <param name="partial" value="0" />
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89 <output name="summary" file="fastx_barcode_splitter1.out" />
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90 <output_collection name="split_output" type="list">
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91 <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
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92 <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
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93 <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
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94 <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
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95 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
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96 </output_collection>
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97 </test>
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98
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99 <test>
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100 <!-- Split a FASTQ file, using separate index read -->
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101 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
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102 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
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103 <param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" />
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104 <param name="barcodeLocation" value="idxfile" />
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105 <param name="mismatches" value="2" />
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106 <param name="partial" value="0" />
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107 <output name="summary" file="fastx_barcode_splitter1.out" />
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108 <output_collection name="split_output" type="list">
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109 <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
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110 <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
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111 <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
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112 <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
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113 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
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114 </output_collection>
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115 </test>
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116 </tests>
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117
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118 <help><![CDATA[
0
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119 **What it does**
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120
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121 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.
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122
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123 --------
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124
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125 **Barcode file Format**
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126
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127 Barcode files are simple text files.
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128 Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
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129 Example::
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130
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131 #This line is a comment (starts with a 'number' sign)
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132 BC1 GATCT
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133 BC2 ATCGT
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134 BC3 GTGAT
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135 BC4 TGTCT
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136
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137 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
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138 Sequences matching the barcode will be stored in the appropriate file.
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139
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140 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
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141
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142 The output of this tool is an HTML file, displaying the split counts and the file locations.
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143
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144 **Output Example**
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145
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146 .. image:: barcode_splitter_output_example.png
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147
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148 ------
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149
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150 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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151
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152 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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153 ]]></help>
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154 <expand macro="citations" />
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155 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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156 </tool>