Mercurial > repos > drosofff > yac_clipper
annotate yac.xml @ 0:307cd074fa95 draft
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author | drosofff |
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date | Wed, 27 May 2015 17:40:52 -0400 |
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children | 8a8f62b4bf27 |
rev | line source |
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0
307cd074fa95
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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1 <tool id="yac" name="Clip adapter" version="1.3.3"> |
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2 <description /> |
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3 <command interpreter="python">yac.py --input $input |
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4 --output $output |
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5 --output_format "$out_format" |
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6 --adapter_to_clip $clip_source.clip_sequence |
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7 --min $min |
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8 --max $max |
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9 --Nmode $Nmode |
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10 </command> |
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11 <inputs> |
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12 <param format="fastq" label="Source file" name="input" type="data" /> |
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13 <param label="min size" name="min" size="4" type="integer" value="15" /> |
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14 <param label="max size" name="max" size="4" type="integer" value="36" /> |
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15 <param label="Select output format" name="out_format" type="select"> |
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16 <option selected="true" value="fasta">Fasta format</option> |
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17 <option value="fastq">Fastq format</option> |
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18 </param> |
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19 <param label="Accept reads containing N?" name="Nmode" type="select"> |
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20 <option selected="True" value="accept">accept</option> |
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21 <option value="reject">reject</option> |
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22 </param> |
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23 <conditional name="clip_source"> |
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24 <param help="Built-in adapters or User-provided" label="Source" name="clip_source_list" type="select"> |
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25 <option selected="True" value="prebuilt">Use a built-in adapter (select from the list below)</option> |
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26 <option value="user">Use custom sequence</option> |
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27 </param> |
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28 <when value="prebuilt"> |
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29 <param help="if your adapter is not listed, input your own sequence" label="Select Adapter to clip" name="clip_sequence" type="select"> |
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30 <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option> |
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31 <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option> |
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32 <option selected="True" value="TGGAATTCTCGGGTGCCAAG">Illumina TruSeq TGGAATTCTCGGGTGCCAAG</option> |
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33 <option value="CTGTAGGCACCATCAATCGT">IdT CTGTAGGCACCATCAATCGT</option> |
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34 </param> |
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35 </when> |
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36 <when value="user"> |
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37 <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" /> |
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38 </when> |
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39 </conditional> |
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40 </inputs> |
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41 <outputs> |
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42 <data format="fasta" metadata="input" name="output" /> |
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43 <change_format> |
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44 <when format="fastq" input="out_format" value="fastq" /> |
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45 </change_format> |
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46 </outputs> |
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47 <tests> |
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48 <test> |
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49 <param ftype="fastqsanger" name="input" value="yac.fastq" /> |
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50 <param name="min" value="18" /> |
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51 <param name="max" value="29" /> |
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52 <param name="clip_source_list" value="prebuilt" /> |
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53 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> |
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54 <param name="Nmode" value="accept" /> |
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55 <output file="yac.out" name="output" /> |
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56 </test> |
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57 <test> |
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58 <param ftype="fastqsanger" name="input" value="yac.fastq" /> |
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59 <param name="min" value="18" /> |
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60 <param name="max" value="29" /> |
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61 <param name="clip_source_list" value="prebuilt" /> |
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62 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> |
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63 <param name="Nmode" value="accept" /> |
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64 <param name="out_format" value="fastq" /> |
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65 <output file="yac_fastq.out" name="output" /> |
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66 </test> |
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67 </tests> |
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68 <help> |
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69 This tool clips adapter sequences from a fastq file and outputs either a |
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70 fasta or fastq file of clipped reads with renumbered fasta/fastq headers. |
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71 |
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72 By defualt clipped sequences with unknown nucleotides are kept, but |
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73 can be discarded by setting "Accept reads containing N?" to reject. |
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74 |
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75 Min size and max size filter clipped reads on their size. |
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76 |
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77 Note that unclipped reads that satisfy the min and max size conditions are kept. |
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78 </help> |
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79 </tool> |