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1 <tool id="cshl_fastx_end_trimmer" name="Trim End">
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2 <description>of sequences</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 -t $trimnum -m $minlen -o '$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="trimnum" size="4" type="integer" value="5">
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17 <label>Number of nucleotides to be trimmed</label>
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18 <help>This will trim from the end of the sequences</help>
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19 </param>
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20
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21 <param name="minlen" size="4" type="integer" value="10">
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22 <label>Minimum sequence length</label>
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23 <help>Sequences shorter than this length will be discarded</help>
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24 </param>
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25 </inputs>
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26
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27 <tests>
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28 <test>
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29 <param name="input" value="fastx_trimmer_from_end1.fasta" />
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30 <param name="trimnum" value="2"/>
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31 <param name="minlen" value="16"/>
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32 <output name="output" file="fastx_trimmer_from_end1.out" />
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33 </test>
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34 </tests>
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35
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36 <outputs>
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37 <data format="input" name="output" metadata_source="input"
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38 />
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39 </outputs>
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40 <help>
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41 **What it does**
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42
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43 This tool trims (cut nucleotides from) sequences in a FASTQ/FASTA file from the 3' end.
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44
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45 .. class:: infomark
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46
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47 When trimming a FASTQ file, the quality scores will be trimmed appropriately (to the same length of the corresponding sequence).
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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::
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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 CAGCGAGGCTTTAATGCCATT
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59
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60
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61 Trimming 5 nucleotides from the end, and discarding sequences shorter than 10 , we get the following FASTA file::
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62
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63 >1-1
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64 TATGGTCAGAAACCATATGCAGAGCCTGTAG
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65 >2-1
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66 CAGCGAGGCTTTAATG
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67
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68 Trimming 10 nucleotides from the end, and discarding sequences shorter than 15 , we get the following FASTA file::
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69
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70 >1-1
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71 TATGGTCAGAAACCATATGCAGAGCC
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72
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73 ------
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74
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75 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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76
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77 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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78
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79 </help>
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80 </tool>
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81 <!-- FASTX-Trimmer-End is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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