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comparison fastx_barcode_splitter.xml @ 1:b7b3d008e2d3 draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit e6a486662201362134119c0ddc7151b8dd181ebd
author lparsons
date Tue, 27 Oct 2015 11:47:52 -0400
parents 84bbf4fd24c3
children 32304398ef67
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0:84bbf4fd24c3 1:b7b3d008e2d3
1 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter" force_history_refresh="True"> 1 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter" force_history_refresh="True">
2 <description></description> 2 <description></description>
3 <command interpreter="bash"> 3 <command interpreter="bash"><![CDATA[
4 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $input.extension --mismatches $mismatches --partial $partial 4 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $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 > $output
11 ]]>
11 </command> 12 </command>
12 13
13 <inputs> 14 <inputs>
14 <param format="txt" version="1.1" name="BARCODE" type="data" label="Barcodes to use" /> 15 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
15 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" version="1.1" name="input" type="data" label="Library to split" /> 16 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
16 17
17 <conditional name="refBarcodeLocation"> 18 <conditional name="refBarcodeLocation">
18 <param version="1.1" name="barcodeLocation" type="select" label="Barcodes found at"> 19 <param name="barcodeLocation" type="select" label="Barcodes found at">
19 <option value="bol">Start of sequence (5' end)</option> 20 <option value="bol">Start of sequence (5' end)</option>
20 <option value="eol">End of sequence (3' end)</option> 21 <option value="eol">End of sequence (3' end)</option>
21 <option value="idxfile">Separate index file</option> 22 <option value="idxfile">Separate index file</option>
22 </param> 23 </param>
23 <when value="bol"> 24 <when value="bol">
24 <param version="1.1" name="EOL" type="hidden" value="--bol" /> 25 <param name="EOL" type="hidden" value="--bol" />
25 </when> 26 </when>
26 <when value="eol"> 27 <when value="eol">
27 <param version="1.1" name="EOL" type="hidden" value="--eol" /> 28 <param name="EOL" type="hidden" value="--eol" />
28 </when> 29 </when>
29 <when value="idxfile"> 30 <when value="idxfile">
30 <param version="1.1" 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" />
31 </when> 32 </when>
32 </conditional> 33 </conditional>
33 34
34 <param version="1.1" 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" />
35 36
36 <param version="1.1" 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" />
37 38
38 </inputs> 39 </inputs>
39 40
40 <tests> 41 <outputs>
42 <data format="html" name="output" />
43 </outputs>
44
45 <tests>
41 <test> 46 <test>
42 <!-- Split a FASTQ file --> 47 <!-- Split a FASTQ file -->
43 <param version="1.1" name="BARCODE" value="fastx_barcode_splitter1.txt" /> 48 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
44 <param version="1.1" name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> 49 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
45 <param version="1.1" name="EOL" value="Start of sequence (5' end)" /> 50 <param name="barcodeLocation" value="bol" />
46 <param version="1.1" name="mismatches" value="2" /> 51 <param name="mismatches" value="2" />
47 <param version="1.1" name="partial" value="0" /> 52 <param name="partial" value="0" />
48 <output version="1.1" name="output" file="fastx_barcode_splitter1.out" /> 53 <output name="output" file="fastx_barcode_splitter1.out" />
49 </test> 54 </test>
50 </tests> 55 </tests>
51 56
52 <outputs> 57 <help><![CDATA[
53 <data version="1.1" format="html" name="output" />
54 </outputs>
55 <help>
56
57 **What it does** 58 **What it does**
58 59
59 This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria. 60 This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria.
60 61
61 -------- 62 --------
69 #This line is a comment (starts with a 'number' sign) 70 #This line is a comment (starts with a 'number' sign)
70 BC1 GATCT 71 BC1 GATCT
71 BC2 ATCGT 72 BC2 ATCGT
72 BC3 GTGAT 73 BC3 GTGAT
73 BC4 TGTCT 74 BC4 TGTCT
74 75
75 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). 76 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
76 Sequences matching the barcode will be stored in the appropriate file. 77 Sequences matching the barcode will be stored in the appropriate file.
77 78
78 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. 79 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
79 80
80 The output of this tool is an HTML file, displaying the split counts and the file names. 81 The output of this tool is an HTML file, displaying the split counts and the file names.
81 In addition, each fastq file produced will be loaded into the galaxy history automatically. 82 In addition, each fastq file produced will be loaded into the galaxy history automatically.
83 ]]>
84 </help>
82 85
86 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
87 <citations>
88 <citation type="bibtex">
89 @misc{gordon_fastx-toolkit_????,
90 title = {{FASTX}-{Toolkit}},
91 url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
92 author = {Gordon, Assaf}
93 }
94 </citation>
95 </citations>
83 96
84 ------
85
86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
87
88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
89
90 </help>
91 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
92 </tool> 97 </tool>