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annotate fastx_trimmer.xml @ 2:97f0b63ae7cf draft

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author devteam
date Tue, 13 Oct 2015 12:42:13 -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>
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7 <![CDATA[
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8 zcat -f < '$input' | fastx_trimmer -v -f $first -l $last -o '$output'
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9 #if $input.ext == "fastqsanger":
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10 -Q 33
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11 #end if
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12 ]]>
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13 </command>
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14
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15 <inputs>
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16 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" />
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17
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18 <param name="first" type="integer" value="1">
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19 <label>First base to keep</label>
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20 </param>
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21
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22 <param name="last" type="integer" value="21">
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23 <label>Last base to keep</label>
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24 </param>
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25 </inputs>
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26 <outputs>
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27 <data format_source="input" name="output" metadata_source="input" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
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32 <param name="input" value="fastx_trimmer1.fasta" />
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33 <param name="first" value="5"/>
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34 <param name="last" value="36"/>
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35 <output name="output" ftype="fasta" file="fastx_trimmer1.out" />
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36 </test>
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37 <test>
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38 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
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39 <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
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40 <param name="first" value="1"/>
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41 <param name="last" value="27"/>
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42 <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
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43 </test>
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44 </tests>
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45 <help>
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46 **What it does**
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47
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48 This tool trims (cut bases from) sequences in a FASTA/Q file.
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49
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50 --------
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51
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52 **Example**
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53
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54 Input Fasta file (with 36 bases in each sequences)::
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55
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56 >1-1
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57 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
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58 >2-1
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59 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
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60
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61
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62 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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63
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64 >1-1
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65 TATGGTCAGAAACCATATGCA
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66 >2-1
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67 CAGCGAGGCTTTAATGCCATT
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68
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69 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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70
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71 >1-1
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72 TCAGA
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73 >2-1
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74 AGGCT
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75
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76 ------
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77
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78 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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79
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80 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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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>