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comparison fastx_barcode_splitter.xml @ 4:e3d91cb9f196 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:50:59 -0400
parents 3b0cd3132ddc
children da00153634dc
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3:3b0cd3132ddc 4:e3d91cb9f196
1 <tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter"> 1 <tool id="cshl_fastx_barcode_splitter" version="1.0.1" name="Barcode Splitter">
2 <description></description> 2 <description></description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' </command> 6 <expand macro="requirements" />
7 <command detect_errors="aggressive"><![CDATA[
8 mkdir split &&
9 @CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE'
10 --prefix 'split/'
11 --suffix '.$input.extension'
12 --mismatches $mismatches
13 --partial $partial
14 #if $refBarcodeLocation.barcodeLocation == "idxfile":
15 --idxfile '$refBarcodeLocation.idxfile'
16 --idxidstrip $refBarcodeLocation.idxidstrip
17 #else:
18 $refBarcodeLocation.EOL
19 #end if
20 > '$summary'
21 ]]></command>
22 <inputs>
23 <param name="BARCODE" type="data" format="txt" label="Barcodes to use" />
24 <param name="input" type="data" format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" label="Library to split" />
7 25
8 <inputs> 26 <conditional name="refBarcodeLocation">
9 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> 27 <param name="barcodeLocation" type="select" label="Barcodes found at">
10 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> 28 <option value="bol">Start of sequence (5' end)</option>
29 <option value="eol">End of sequence (3' end)</option>
30 <option value="idxfile">Separate index file</option>
31 </param>
32 <when value="bol">
33 <param name="EOL" type="hidden" value="--bol" />
34 </when>
35 <when value="eol">
36 <param name="EOL" type="hidden" value="--eol" />
37 </when>
38 <when value="idxfile">
39 <param argument="--idxidstrip" type="integer" value="1" label="Characters to strip from the end of the sequence id before matching" />
40 <param argument="--idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
41 </when>
42 </conditional>
43 <param argument="--mismatches" type="integer" value="0" label="Number of allowed mismatches" />
44 <param argument="--partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" />
45 </inputs>
11 46
12 <param name="EOL" type="select" label="Barcodes found at"> 47 <outputs>
13 <option value="--bol">Start of sequence (5' end)</option> 48 <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" />
14 <option value="--eol">End of sequence (3' end)</option> 49 <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}">
15 </param> 50 <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" />
51 </collection>
52 </outputs>
16 53
17 <param name="mismatches" type="integer" value="2" label="Number of allowed mismatches" />
18
19 <param name="partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" />
20 </inputs>
21 <outputs>
22 <data format="html" name="output" />
23 </outputs>
24 <tests> 54 <tests>
25 <test> 55 <test>
26 <!-- Split a FASTQ file --> 56 <!-- Split a FASTQ file -->
27 <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> 57 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
28 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> 58 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
29 <param name="EOL" value="Start of sequence (5' end)" /> 59 <param name="barcodeLocation" value="bol" />
30 <param name="mismatches" value="2" /> 60 <param name="mismatches" value="2" />
31 <param name="partial" value="0" /> 61 <param name="partial" value="0" />
32 <output name="output" file="fastx_barcode_splitter1.out" /> 62 <output name="summary" file="fastx_barcode_splitter1.out" />
63 <output_collection name="split_output" type="list">
64 <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
65 <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
66 <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
67 <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
68 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
69 </output_collection>
70 </test>
71
72 <test>
73 <!-- Split a FASTQ file, using separate index read -->
74 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
75 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
76 <param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" />
77 <param name="barcodeLocation" value="idxfile" />
78 <param name="mismatches" value="2" />
79 <param name="partial" value="0" />
80 <output name="summary" file="fastx_barcode_splitter1.out" />
81 <output_collection name="split_output" type="list">
82 <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
83 <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
84 <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
85 <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
86 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
87 </output_collection>
33 </test> 88 </test>
34 </tests> 89 </tests>
35 <help> 90
91 <help><![CDATA[
36 **What it does** 92 **What it does**
37 93
38 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. 94 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.
39 95
40 -------- 96 --------
60 116
61 **Output Example** 117 **Output Example**
62 118
63 .. image:: barcode_splitter_output_example.png 119 .. image:: barcode_splitter_output_example.png
64 120
65
66 ------ 121 ------
67 122
68 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 123 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
69 124
70 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 125 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
71 </help> 126 ]]></help>
127 <expand macro="citations" />
72 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 128 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
73 </tool> 129 </tool>