Mercurial > repos > devteam > fastx_barcode_splitter
annotate fastx_barcode_splitter.xml @ 3:8abdedf55101 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:38:37 -0500 |
parents | c46a5807f2b6 |
children | 015dc921d814 |
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0 | 1 <tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter"> |
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8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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2 <description></description> |
0 | 3 <requirements> |
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
5 </requirements> | |
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8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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6 <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' </command> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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7 |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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8 <inputs> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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9 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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10 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> |
0 | 11 |
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8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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12 <param name="EOL" type="select" label="Barcodes found at"> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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13 <option value="--bol">Start of sequence (5' end)</option> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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14 <option value="--eol">End of sequence (3' end)</option> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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15 </param> |
0 | 16 |
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8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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17 <param name="mismatches" type="integer" value="2" label="Number of allowed mismatches" /> |
0 | 18 |
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8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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19 <param name="partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" /> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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20 </inputs> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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21 <outputs> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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22 <data format="html" name="output" /> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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23 </outputs> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
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24 <tests> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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25 <test> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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26 <!-- Split a FASTQ file --> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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27 <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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28 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
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29 <param name="EOL" value="Start of sequence (5' end)" /> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
2
diff
changeset
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30 <param name="mismatches" value="2" /> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
2
diff
changeset
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31 <param name="partial" value="0" /> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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32 <output name="output" file="fastx_barcode_splitter1.out" /> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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33 </test> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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changeset
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34 </tests> |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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35 <help> |
0 | 36 **What it does** |
37 | |
38 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. | |
39 | |
40 -------- | |
41 | |
42 **Barcode file Format** | |
43 | |
44 Barcode files are simple text files. | |
45 Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character. | |
46 Example:: | |
47 | |
48 #This line is a comment (starts with a 'number' sign) | |
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8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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49 BC1 GATCT |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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50 BC2 ATCGT |
8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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51 BC3 GTGAT |
0 | 52 BC4 TGTCT |
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8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
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53 |
0 | 54 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). |
55 Sequences matching the barcode will be stored in the appropriate file. | |
56 | |
57 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. | |
58 | |
59 The output of this tool is an HTML file, displaying the split counts and the file locations. | |
60 | |
61 **Output Example** | |
62 | |
2 | 63 .. image:: barcode_splitter_output_example.png |
0 | 64 |
65 | |
66 ------ | |
67 | |
68 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
69 | |
70 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
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8abdedf55101
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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71 </help> |
0 | 72 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |
73 </tool> |