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annotate yac.xml @ 7:396bc2c718a1 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit a30e10dfaf7ba8a1b6e38075f058b11186790c74
author artbio
date Tue, 29 Nov 2022 08:58:44 +0000
parents acbf910cd2ae
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7
396bc2c718a1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit a30e10dfaf7ba8a1b6e38075f058b11186790c74
artbio
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1 <tool id="yac" name="Clip adapter" version="2.5.1">
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 />
5
6bfb7e333280 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
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3 <requirements>
6bfb7e333280 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
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4 <requirement type="package" version="3.7.6">python</requirement>
6bfb7e333280 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
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5 </requirements>
2
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6 <command detect_errors="exit_code"><![CDATA[
da08e89abd18 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 4767dcb09e8bb26a38ea458b2cf4f9d98a4afb95
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7 python $__tool_directory__/yac.py
da08e89abd18 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 4767dcb09e8bb26a38ea458b2cf4f9d98a4afb95
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8 --input $input
3
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9 --output 'clip.tmp'
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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10 --output_format
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11 #if $out_format == 'fasta' or $out_format == 'fastagz':
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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12 'fasta'
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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13 #else
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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14 'fastq'
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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15 #end if
2
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16 --adapter_to_clip $clip_source.clip_sequence
da08e89abd18 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 4767dcb09e8bb26a38ea458b2cf4f9d98a4afb95
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17 --min $min
da08e89abd18 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 4767dcb09e8bb26a38ea458b2cf4f9d98a4afb95
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18 --max $max
3
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19 --Nmode $Nmode &&
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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20 #if ($out_format == 'fastagz') or ($out_format == 'fastqgz'):
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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21 gzip -c 'clip.tmp' > $output
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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22 #else
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23 mv clip.tmp $output
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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24 #end if
2
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25 ]]></command>
0
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26 <inputs>
3
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27 <param format="fasta,fastq" label="Source file" name="input" type="data" />
0
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28 <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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29 <param label="max size" name="max" size="4" type="integer" value="36" />
3
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30 <param label="Select output format" name="out_format" type="select"
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31 help="be careful not to select a fastq format for your output if your input has a fasta format">
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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32 <option value="fasta">Fasta</option>
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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33 <option value="fastq" selected="true" >Fastq (Sanger)</option>
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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34 <option value="fastagz">gzipped Fasta</option>
94d67b195acd planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
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35 <option value="fastqgz">gzipped Fastq (Sanger)</option>
0
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36 </param>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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37 <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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38 <option selected="True" value="accept">accept</option>
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39 <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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40 </param>
ad6b978daa2e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
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41 <conditional name="clip_source">
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42 <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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43 <option selected="True" value="prebuilt">Use a built-in adapter (select from the list below)</option>
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44 <option value="user">Use custom sequence</option>
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45 </param>
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46 <when value="prebuilt">
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47 <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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48 <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option>
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49 <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option>
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50 <option selected="True" value="TGGAATTCTCGGGTGCCAAG">Illumina TruSeq TGGAATTCTCGGGTGCCAAG</option>
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51 <option value="CTGTAGGCACCATCAATCGT">IdT CTGTAGGCACCATCAATCGT</option>
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52 </param>
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53 </when>
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54 <when value="user">
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55 <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" />
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56 </when>
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57 </conditional>
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58 </inputs>
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59 <outputs>
3
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60 <data format_source="input" metadata_source="input" name="output" label="Clipped ${input.name}-then-${out_format}">
0
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61 <change_format>
1
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62 <when input="out_format" value="fasta" format="fasta" />
3
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63 <when input="out_format" value="fastq" format="fastqsanger" />
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64 <when input="out_format" value="fastagz" format="fasta.gz" />
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65 <when input="out_format" value="fastqgz" format="fastqsanger.gz" />
0
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66 </change_format>
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67 </data>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param ftype="fastqsanger" name="input" value="yac.fastq" />
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72 <param name="min" value="18" />
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73 <param name="max" value="29" />
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74 <param name="clip_source_list" value="prebuilt" />
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75 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
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76 <param name="Nmode" value="accept" />
3
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77 <param name="out_format" value="fastq" />
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78 <output file="out.fastqsanger" name="output" />
0
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79 </test>
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80 <test>
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81 <param ftype="fastqsanger" name="input" value="yac.fastq" />
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82 <param name="min" value="18" />
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83 <param name="max" value="29" />
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84 <param name="clip_source_list" value="prebuilt" />
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85 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
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86 <param name="Nmode" value="accept" />
3
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87 <param name="out_format" value="fasta" />
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88 <output file="out.fasta" name="output" />
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89 </test>
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90 <test>
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91 <param ftype="fastqsanger.gz" name="input" value="yac.fastqsanger.gz" />
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92 <param name="min" value="18" />
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93 <param name="max" value="29" />
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94 <param name="clip_source_list" value="prebuilt" />
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95 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
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96 <param name="Nmode" value="accept" />
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97 <param name="out_format" value="fastqgz" />
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98 <output file="out.fastqsanger.gz" name="output" decompress="True" />
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99 </test>
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100 <test>
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101 <param ftype="fastqsanger.gz" name="input" value="yac.fastqsanger.gz" />
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102 <param name="min" value="18" />
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103 <param name="max" value="29" />
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104 <param name="clip_source_list" value="prebuilt" />
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105 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
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106 <param name="Nmode" value="accept" />
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107 <param name="out_format" value="fastagz" />
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108 <output file="out.fasta.gz" name="output" decompress="True" />
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109 </test>
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110 <test>
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111 <param ftype="fasta.gz" name="input" value="yac.fasta.gz" />
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112 <param name="min" value="18" />
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113 <param name="max" value="29" />
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114 <param name="clip_source_list" value="prebuilt" />
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115 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
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116 <param name="out_format" value="fasta" />
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117 <param name="Nmode" value="accept" />
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118 <output file="out.fasta" name="output" />
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119 </test>
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120 <test>
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121 <param ftype="fasta.gz" name="input" value="yac.fasta.gz" />
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122 <param name="min" value="18" />
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123 <param name="max" value="29" />
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124 <param name="clip_source_list" value="prebuilt" />
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125 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
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126 <param name="Nmode" value="accept" />
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127 <param name="out_format" value="fastagz" />
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128 <output file="out.fasta.gz" name="output" decompress="True" />
0
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129 </test>
4
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130 <test>
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131 <param ftype="fastqsanger.gz" name="input" value="yac_with_empty_reads.fastqsanger.gz" />
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132 <param name="min" value="18" />
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133 <param name="max" value="30" />
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134 <param name="clip_source_list" value="prebuilt" />
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135 <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG" />
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136 <param name="Nmode" value="accept" />
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137 <param name="out_format" value="fastagz" />
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138 <output file="out_with_empty_reads.fasta.gz" name="output" decompress="True" />
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139 </test>
0
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140 </tests>
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141 <help>
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142
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143 **What it does**
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144
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145 + Clips adapter sequences
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146 + Renumbers sequence headers
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147 + Filters sequences on their size
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148 + Filters sequences containing unknown nucleotides (optional)
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149
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150 -------
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151
7
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152 yac_clipper clips 7nt long motives in 5' of adapter sequences. *It is accepting 1 mismatch in the searched 7nt motif.*
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153
0
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154 **Inputs**
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155
3
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156 1. A fastq or fasta file of reads to be clipped
0
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157 2. Select the size of the reads to be kept
3
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158 3. Select an output format. When input is a fastq file, this may be fastq or fasta, whereas
7
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159 when input is a fasta file, this only may be a fasta.
0
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160 4. Select whether you wish or do not wish to keep clipped sequences with unknown nucleotides (N)
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161 5. Select a pre-built adapter sequence or enter your own sequence (at least 7 nucleotides long)
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162
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163 -------
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164
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165 **Output**
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166
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167 A fastq or fasta file containing clipped sequences satisfying the selected criteria.
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168
2
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169 </help>
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170 <citations />
0
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171 </tool>