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annotate fastx_barcode_splitter.xml @ 3:3b0cd3132ddc draft

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author devteam
date Tue, 13 Oct 2015 12:40:38 -0400
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1 <tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
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5 </requirements>
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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>
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7
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8 <inputs>
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9 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
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10 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
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11
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12 <param name="EOL" type="select" label="Barcodes found at">
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13 <option value="--bol">Start of sequence (5' end)</option>
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14 <option value="--eol">End of sequence (3' end)</option>
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15 </param>
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16
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17 <param name="mismatches" type="integer" value="2" label="Number of allowed mismatches" />
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19 <param name="partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" />
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20 </inputs>
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21 <outputs>
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22 <data format="html" name="output" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <!-- Split a FASTQ file -->
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27 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
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28 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
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29 <param name="EOL" value="Start of sequence (5' end)" />
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30 <param name="mismatches" value="2" />
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31 <param name="partial" value="0" />
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32 <output name="output" file="fastx_barcode_splitter1.out" />
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33 </test>
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34 </tests>
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35 <help>
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36 **What it does**
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37
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38 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.
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39
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40 --------
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41
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42 **Barcode file Format**
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43
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44 Barcode files are simple text files.
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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.
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46 Example::
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47
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48 #This line is a comment (starts with a 'number' sign)
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49 BC1 GATCT
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50 BC2 ATCGT
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51 BC3 GTGAT
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52 BC4 TGTCT
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53
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54 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
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55 Sequences matching the barcode will be stored in the appropriate file.
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56
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57 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
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58
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59 The output of this tool is an HTML file, displaying the split counts and the file locations.
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60
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61 **Output Example**
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62
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63 .. image:: barcode_splitter_output_example.png
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66 ------
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67
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68 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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69
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70 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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71 </help>
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72 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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73 </tool>