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