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