annotate fastx_renamer.xml @ 1:e7c65e398bdd draft default tip

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author idot
date Wed, 10 Jul 2013 06:16:21 -0400
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1 <tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
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2 <description></description>
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3 <command>
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4 cat '$input' |
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5 fastx_renamer
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6 #if $input.ext == "fastqsanger":
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7 -Q 33
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8 #elif $input.ext == "fastq":
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9 -Q 64
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10 #end if
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11 -n $TYPE -o '$output' -v
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12 </command>
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13 <inputs>
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14 <param format="fastq,fastqsanger,fasta" name="input" type="data" label="FASTQ/A Library to rename" />
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15
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16 <param name="TYPE" type="select" label="Rename sequence identifiers to">
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17 <option value="SEQ">Nucleotides sequence</option>
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18 <option value="COUNT">Numeric Counter</option>
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19 </param>
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20 </inputs>
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21 <tests>
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22 <test>
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23 <param name="input" value="fastx_renamer1.fastq" ftype="fastq"/>
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24 <param name="TYPE" value="SEQ" />
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25 <output name="output" file="fastx_renamer1.out" />
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26 </test>
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27 </tests>
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28
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29 <outputs>
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30 <data format="input" name="output" metadata_source="input" />
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31 </outputs>
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32
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33 <help>
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34
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35 **What it does**
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36
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37 This tool renames the sequence identifiers in a FASTQ/A file.
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38
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39 .. class:: infomark
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40
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41 Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc).
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42
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43 --------
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44
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45 **Example**
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46
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47 The following Solexa-FASTQ file::
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48
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49 @CSHL_4_FC042GAMMII_2_1_517_596
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50 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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51 +CSHL_4_FC042GAMMII_2_1_517_596
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52 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
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53
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54 Renamed to **nucleotides sequence**::
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55
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56 @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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57 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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58 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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59 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
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60
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61 Renamed to **numeric counter**::
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62
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63 @1
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64 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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65 +1
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66 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
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67
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68 ------
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69
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70 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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71
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72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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73 </help>
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74 </tool>
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75 <!-- FASTX-renamer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->