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Alternative barcode splitters that move selected results to the users history.
author Jim Johnson <jj@umn.edu>
date Tue, 19 Jul 2011 13:03:32 -0500
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1 <tool id="cshl_fastx_barcode_splitter_single" name="Barcode Splitter (Single)">
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2 <description></description>
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3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
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4 <command interpreter="python">fastx_barcode_splitter_single_galaxy_wrapper.py
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5 $matched_output
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6 $unmatched_output
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7 "$input.ext"
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8 --barcodes='$barcode'
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9 $input "$input.name"
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10 --mismatches $mismatches --partial $partial $EOL
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11 </command>
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12
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13 <inputs>
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14 <!-- <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> -->
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15 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
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16
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17 <param name="EOL" type="select" label="Barcodes found at">
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18 <option value="--bol">Start of sequence (5' end)</option>
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19 <option value="--eol">End of sequence (3' end)</option>
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20 </param>
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21
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22 <param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" />
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23
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24 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
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25
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26 <param name="barcode" type="text" label="Barcode to extract" />
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27
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28 <!--
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29 <param name="barcodes" type="select" multiple="true" label="Select barcodes to add as new datasets to history">
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30 <options from_dataset="BARCODE">
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31 <column name="name" index="0"/>
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32 <column name="value" index="0"/>
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33 <filter type="unique_value" name="unq_bc" column="0" />
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34 <filter type="add_value" name="unmatched" value="unmatched"/>
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35 </options>
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36 </param>
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37 -->
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38 </inputs>
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39
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40 <outputs>
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41 <data format_source="input" name="matched_output" label="Barcode Splitter on ${input.name} (Matching sequences)" />
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42 <data format_source="input" name="unmatched_output" label="Barcode Splitter on ${input.name} (Unmatched sequences)" />
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43 </outputs>
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44
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45 <tests>
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46 </tests>
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47
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48 <help>
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49
bc23f6946bb8 Alternative barcode splitters that move selected results to the users history.
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50 **What it does**
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51
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52 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into two files using a barcode as the split criteria.
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53
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54 --------
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55
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56 A new FASTQ file will be created (with the barcode's identifier as part of the file name).
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57 Sequences matching the barcode will be stored in the appropriate file.
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58
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59 An additional FASTQ file will be created (the 'unmatched' file), where sequences not matching this barcode will be stored.
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60
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61 </help>
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62 </tool>
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63 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->