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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
author lparsons
date Mon, 02 May 2016 17:04:32 -0400
parents e7b7cdc1834d
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3:e7b7cdc1834d 4:0fb7e9130a70
1 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter"> 1 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.2" name="Barcode Splitter">
2 <description></description> 2 <description></description>
3 <command interpreter="bash"><![CDATA[ 3 <command interpreter="bash" detect_errors="aggressive"><![CDATA[
4 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "split/" $input.extension --mismatches $mismatches --partial $partial 4 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "split/" $input.extension --mismatches $mismatches --partial $partial
5 #if $refBarcodeLocation.barcodeLocation == "idxfile": 5 #if $refBarcodeLocation.barcodeLocation == "idxfile":
6 --idxfile $refBarcodeLocation.idxfile 6 --idxfile $refBarcodeLocation.idxfile
7 #else: 7 #else:
8 $refBarcodeLocation.EOL 8 $refBarcodeLocation.EOL
9 #end if 9 #end if
10 > $output 10 > $summary
11 ]]> 11 ]]>
12 </command> 12 </command>
13 13
14 <inputs> 14 <inputs>
15 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> 15 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
16 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> 16 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
17 17
18 <conditional name="refBarcodeLocation"> 18 <conditional name="refBarcodeLocation">
19 <param name="barcodeLocation" type="select" label="Barcodes found at"> 19 <param name="barcodeLocation" type="select" label="Barcodes found at">
20 <option value="bol">Start of sequence (5' end)</option> 20 <option value="bol">Start of sequence (5' end)</option>
21 <option value="eol">End of sequence (3' end)</option> 21 <option value="eol">End of sequence (3' end)</option>
22 <option value="idxfile">Separate index file</option> 22 <option value="idxfile">Separate index file</option>
23 </param> 23 </param>
24 <when value="bol"> 24 <when value="bol">
25 <param name="EOL" type="hidden" value="--bol" /> 25 <param name="EOL" type="hidden" value="--bol" />
26 </when> 26 </when>
27 <when value="eol"> 27 <when value="eol">
28 <param name="EOL" type="hidden" value="--eol" /> 28 <param name="EOL" type="hidden" value="--eol" />
29 </when> 29 </when>
30 <when value="idxfile"> 30 <when value="idxfile">
31 <param name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" /> 31 <param name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
32 </when> 32 </when>
33 </conditional> 33 </conditional>
34 34
35 <param name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" /> 35 <param name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
36 36
37 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" /> 37 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
38 38
39 </inputs> 39 </inputs>
40 40
41 <outputs> 41 <outputs>
42 <data format="html" name="output"> 42 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: Summary" />
43 <discover_datasets pattern="__designation_and_ext__" directory="split" visible="true" label="${tool.name}: ${designation}"/> 43 <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}">
44 </data> 44 <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" label="${designation}"/>
45 </outputs> 45 </collection>
46 </outputs>
46 47
47 <tests> 48 <tests>
48 <test> 49 <test>
49 <!-- Split a FASTQ file --> 50 <!-- Split a FASTQ file -->
50 <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> 51 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
51 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> 52 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
52 <param name="barcodeLocation" value="bol" /> 53 <param name="barcodeLocation" value="bol" />
53 <param name="mismatches" value="2" /> 54 <param name="mismatches" value="2" />
54 <param name="partial" value="0" /> 55 <param name="partial" value="0" />
55 <output name="output" file="fastx_barcode_splitter1.out"> 56 <output name="summary" file="fastx_barcode_splitter1.out" />
56 <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" /> 57 <collection name="output" type="list">
57 <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" /> 58 <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
58 <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" /> 59 <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
59 <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" /> 60 <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
60 <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" /> 61 <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
61 </output> 62 <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
62 </test> 63 </collection>
63 <test> 64 </test>
64 <!-- Split a FASTQ file, using separate index read --> 65
65 <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> 66 <test>
66 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> 67 <!-- Split a FASTQ file, using separate index read -->
67 <param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" /> 68 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
68 <param name="barcodeLocation" value="idxfile" /> 69 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
69 <param name="mismatches" value="2" /> 70 <param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" />
70 <param name="partial" value="0" /> 71 <param name="barcodeLocation" value="idxfile" />
71 <output name="output" file="fastx_barcode_splitter1.out"> 72 <param name="mismatches" value="2" />
72 <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" /> 73 <param name="partial" value="0" />
73 <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" /> 74 <output name="output" file="fastx_barcode_splitter1.out" />
74 <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" /> 75 <collection name="split_output" type="list">
75 <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" /> 76 <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
76 <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" /> 77 <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
77 </output> 78 <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
78 </test> 79 <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
79 </tests> 80 <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
81 </collection>
82 </test>
83 </tests>
80 84
81 <help><![CDATA[ 85 <help><![CDATA[
82 **What it does** 86 **What it does**
83 87
84 This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria. 88 This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria.
90 Barcode files are simple text files. 94 Barcode files are simple text files.
91 Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character. 95 Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
92 Example:: 96 Example::
93 97
94 #This line is a comment (starts with a 'number' sign) 98 #This line is a comment (starts with a 'number' sign)
95 BC1 GATCT 99 BC1 GATCT
96 BC2 ATCGT 100 BC2 ATCGT
97 BC3 GTGAT 101 BC3 GTGAT
98 BC4 TGTCT 102 BC4 TGTCT
99 103
100 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). 104 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
101 Sequences matching the barcode will be stored in the appropriate file. 105 Sequences matching the barcode will be stored in the appropriate file.
102 106
103 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. 107 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
104 108
105 The output of this tool is an HTML file, displaying the split counts and the file names. 109 The output of this tool is a summary tabel displaying the split counts for each barcode identifier.
106 In addition, each fastq file produced will be loaded into the galaxy history automatically. 110 In addition, each fastq file produced will be loaded into the galaxy history as part of a collection list.
107 ]]> 111 ]]>
108 </help> 112 </help>
109 113
110 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 114 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
111 <citations> 115 <citations>
112 <citation type="bibtex"> 116 <citation type="bibtex">
113 @misc{gordon_fastx-toolkit_????, 117 @misc{gordon_fastx-toolkit_????,
114 title = {{FASTX}-{Toolkit}}, 118 title = {{FASTX}-{Toolkit}},
115 url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html}, 119 url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
116 author = {Gordon, Assaf} 120 author = {Gordon, Assaf}
117 } 121 }
118 </citation> 122 </citation>
119 </citations> 123 </citations>
120 124
121 </tool> 125 </tool>