Mercurial > repos > artbio > yac_clipper

annotate yac.xml @ 0:ad6b978daa2e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
author artbio
date Wed, 26 Jul 2017 13:35:39 -0400
parents
children 7c913274e22a
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0
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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1 <tool id="yac" name="Clip adapter" version="2.0.0">
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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2 <description />
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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3 <command interpreter="python">yac.py --input $input
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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4 --output $output
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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5 --output_format "$out_format"
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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6 --adapter_to_clip $clip_source.clip_sequence
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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7 --min $min
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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8 --max $max
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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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" />
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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13 <param label="min size" name="min" size="4" type="integer" value="15" />
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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14 <param label="max size" name="max" size="4" type="integer" value="36" />
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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15 <param label="Select output format" name="out_format" type="select">
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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16 <option selected="true" value="fasta">Fasta format</option>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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17 <option value="fastq">Fastq format</option>
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18 </param>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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19 <param label="Accept reads containing N?" name="Nmode" type="select">
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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20 <option selected="True" value="accept">accept</option>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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21 <option value="reject">reject</option>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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22 </param>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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23 <conditional name="clip_source">
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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24 <param help="Built-in adapters or User-provided" label="Source" name="clip_source_list" type="select">
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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25 <option selected="True" value="prebuilt">Use a built-in adapter (select from the list below)</option>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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26 <option value="user">Use custom sequence</option>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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27 </param>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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28 <when value="prebuilt">
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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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">
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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30 <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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31 <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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32 <option selected="True" value="TGGAATTCTCGGGTGCCAAG">Illumina TruSeq TGGAATTCTCGGGTGCCAAG</option>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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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" />
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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38 </when>
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39 </conditional>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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40 </inputs>
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41 <outputs>
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42 <data format="fasta" metadata_source="input" name="output" label="Clipping of ${input.name}">
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43 <change_format>
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44 <when input="out_format" value="fastq" format="fastq" />
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45 </change_format>
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46 </data>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param ftype="fastqsanger" name="input" value="yac.fastq" />
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51 <param name="min" value="18" />
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52 <param name="max" value="29" />
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53 <param name="clip_source_list" value="prebuilt" />
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54 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
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55 <param name="Nmode" value="accept" />
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56 <output file="yac.out" name="output" />
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57 </test>
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58 <test>
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59 <param ftype="fastqsanger" name="input" value="yac.fastq" />
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60 <param name="min" value="18" />
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61 <param name="max" value="29" />
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62 <param name="clip_source_list" value="prebuilt" />
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63 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
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64 <param name="Nmode" value="accept" />
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65 <param name="out_format" value="fastq" />
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66 <output file="yac_fastq.out" name="output" />
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67 </test>
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68 </tests>
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69 <help>
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70
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71 **What it does**
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72
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73 + Clips adapter sequences
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74 + Renumbers sequence headers
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75 + Filters sequences on their size
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76 + Filters sequences containing unknown nucleotides (optional)
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77
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78 -------
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79
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80 **Inputs**
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81
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82 1. A fastq file of reads to be clipped
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83 2. Select the size of the reads to be kept
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84 3. Select an output format when input is a fastq file (this may be fastq or fastq)
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85 4. Select whether you wish or do not wish to keep clipped sequences with unknown nucleotides (N)
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86 5. Select a pre-built adapter sequence or enter your own sequence (at least 7 nucleotides long)
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87
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88 -------
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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89
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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90 **Output**
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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91
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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92 A fastq or fasta file containing clipped sequences satisfying the selected criteria.
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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93
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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94 </help>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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95 </tool>