annotate fastx_trimmer.xml @ 0:9cb372481a71

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author devteam
date Wed, 25 Sep 2013 11:21:27 -0400
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1 <tool id="cshl_fastx_trimmer" version="1.0.0" name="Trim sequences">
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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>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output
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7 #if $input.ext == "fastqsanger":
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8 -Q 33
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9 #end if
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10 </command>
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11
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12 <inputs>
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13 <param format="fasta,fastqsolexa,fastqsanger" version="1.0.0" name="input" type="data" label="Library to clip" />
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14
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15 <param version="1.0.0" name="first" size="4" type="integer" value="1">
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16 <label>First base to keep</label>
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17 </param>
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18
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19 <param version="1.0.0" name="last" size="4" type="integer" value="21">
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20 <label>Last base to keep</label>
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21 </param>
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22 </inputs>
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23
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24 <tests>
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25 <test>
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26 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
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27 <param version="1.0.0" name="input" value="fastx_trimmer1.fasta" />
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28 <param version="1.0.0" name="first" value="5"/>
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29 <param version="1.0.0" name="last" value="36"/>
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30 <output version="1.0.0" name="output" file="fastx_trimmer1.out" />
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31 </test>
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32 <test>
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33 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
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34 <param version="1.0.0" name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
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35 <param version="1.0.0" name="first" value="1"/>
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36 <param version="1.0.0" name="last" value="27"/>
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37 <output version="1.0.0" name="output" file="fastx_trimmer2.out" />
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38 </test>
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39 </tests>
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40
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41 <outputs>
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42 <data format="input" version="1.0.0" name="output" metadata_source="input" />
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43 </outputs>
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44 <help>
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45 **What it does**
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46
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47 This tool trims (cut bases from) sequences in a FASTA/Q file.
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48
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49 --------
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50
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51 **Example**
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52
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53 Input Fasta file (with 36 bases in each sequences)::
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54
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55 >1-1
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56 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
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57 >2-1
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58 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
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59
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60
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61 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
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62
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63 >1-1
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64 TATGGTCAGAAACCATATGCA
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65 >2-1
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66 CAGCGAGGCTTTAATGCCATT
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67
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68 Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
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69
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70 >1-1
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71 TCAGA
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72 >2-1
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73 AGGCT
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74
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75 ------
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76
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77 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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78
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79 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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80
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81 </help>
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82 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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83 </tool>