Mercurial > repos > devteam > fastx_barcode_splitter
comparison fastx_barcode_splitter.xml @ 4:015dc921d814 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
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date | Tue, 08 May 2018 13:27:14 -0400 |
parents | 8abdedf55101 |
children | 4bedca26c133 |
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3:8abdedf55101 | 4:015dc921d814 |
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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> |