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1 <tool id="cshl_fastx_trimmer" name="Trim">
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2 <description>sequences</description>
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3 <command>zcat -f '$input' | fastx_trimmer $GZIPOUT -v -f $first -l $last -o $output</command>
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4
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5 <inputs>
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6 <param format="fasta,fastqsolexa" name="input" type="data" label="Library to clip" />
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7
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8 <param name="first" size="4" type="integer" value="1">
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9 <label>First base to keep</label>
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10 </param>
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11
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12 <param name="last" size="4" type="integer" value="21">
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13 <label>Last base to keep</label>
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14 </param>
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15
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16 <param name="GZIPOUT" type="select" label="Compress output file (using GZIP) ">
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17 <option value="-z">yes</option>
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18 <option value="">no</option>
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19 </param>
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20 </inputs>
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21
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22 <tests>
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23 <test>
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24 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
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25 <param name="input" value="fastx_trimmer1.fasta" />
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26 <param name="first" value="5"/>
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27 <param name="last" value="36"/>
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28 <param name="GZIPOUT" value=""/>
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29 <output name="output" file="fastx_trimmer1.out" />
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30 </test>
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31 <test>
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32 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
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33 <param name="input" value="fastx_trimmer2.fastq" />
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34 <param name="first" value="1"/>
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35 <param name="last" value="27"/>
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36 <param name="GZIPOUT" value=""/>
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37 <output 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" name="output" label="$input.tag trimmed" 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 </help>
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76 </tool>
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77 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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