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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 18:52:07 -0500
parents c45a263664fd
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c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="cd_hit_dup" name="cd-hit-dup" version="0.0.1">
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <description>
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3 remove duplicates and detect chimaeras in sequencing reads
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="0.5-2012-03-07-fix-dan-gh-0.0.1">cd-hit-auxtools</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 <exit_code range=":-1" />
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11 </stdio>
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12
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 <command><![CDATA[
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 cd-hit-dup
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 -i "${ fastq_input.fastq_input1 }"
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 #if str( $fastq_input.fastq_input_selector ) == "paired":
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17 -i2 "${ fastq_input.fastq_input2 }"
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 #elif str( $fastq_input.filter_chimeras.filter_chimeras_selector ) == "true":
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 -f "true"
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 -s "${ fastq_input.filter_chimeras.min_chimeric_length }"
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 -a "${ fastq_input.filter_chimeras.abundance_cutoff }"
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22 -b "${ fastq_input.filter_chimeras.abundance_ratio }"
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 -p "${ fastq_input.filter_chimeras.dissimilarity_control }"
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24 #end if
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25 -u "${ prefix_length }"
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 -m "${ match_length }"
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 #if str( $mismatches_allowed ) != "":
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28 #if float( str( $mismatches_allowed ) ) == int( float( str( $mismatches_allowed ) ) ):
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 -e "${ int( float( str( $mismatches_allowed ) ) ) }"
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 #else:
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 -e "${ mismatches_allowed }"
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 #end if
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33 #end if
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34 -d "${ description_length }"
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35 -o "output"
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36 ]]>
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37 </command>
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38 <inputs>
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39 <conditional name="fastq_input">
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40 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="For joined Paired-end reads choose Single.">
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41 <option value="paired">Paired</option>
c45a263664fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42 <option value="single" selected="True">Single</option>
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43 </param>
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44 <when value="paired">
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45 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
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46 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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47 </when>
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48 <when value="single">
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49 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select reads" help="Specify dataset with single reads"/>
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50 <conditional name="filter_chimeras">
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51 <param name="filter_chimeras_selector" type="select" label="Filter out chimeric clusters">
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52 <option value="true">Yes</option>
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53 <option value="false" selected="True">No</option>
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54 </param>
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55 <when value="true">
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56 <param name="min_chimeric_length" type="integer" value="30" min="20" label="Minimum length of common sequence shared between a chimeric read and each of its parents" help="-s"/>
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57 <param name="abundance_cutoff" type="integer" value="1" min="1" label="Abundance cutoff" help="-a; Tool Author recommend default of 2, but this would require the chimera itself to need 2 copies"/>
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58 <param name="abundance_ratio" type="integer" value="1" min="1" label="Abundance ratio between a parent read and a chimeric read" help="-b"/>
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59 <param name="dissimilarity_control" type="integer" value="1" min="1" label="Dissimilarity control for chimeric filtering" help="-p"/>
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60 </when>
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61 <when value="false">
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62 <!-- do nothing here -->
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63 </when>
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64 </conditional>
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65 </when>
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66 </conditional>
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67 <param name="prefix_length" type="integer" value="0" min="0" label="Length of prefix to be used in the analysis" help="-u"/>
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68 <param name="match_length" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Match length" help="-m; specifies whether the lengths of two reads should be exactly the same to be considered as duplicates. "/>
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69 <param name="mismatches_allowed" type="float" optional="True" value="" min="0" label="Maximum number/percent of mismatches allowed" help="-e"/>
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70 <param name="description_length" type="integer" value="0" min="0" label="Description length" help="-d; 0 means truncate at the first whitespace character"/>
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71 </inputs>
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72 <outputs>
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73 <data format="fastqsanger" format_source="fastq_input1" name="output_reads" label="${tool.name} on ${on_string} (filtered reads)" from_work_dir="output"/>
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74 <data format="tabular" name="output_duplicate_clusters" label="${tool.name} on ${on_string} (duplicate clusters)" from_work_dir="output.clstr"/>
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75 <data format="tabular" name="output_chimeric_clusters" label="${tool.name} on ${on_string} (chimeric clusters)" from_work_dir="output2.clstr">
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76 <filter>str( fastq_input['filter_chimeras']['filter_chimeras_selector'] ) == "true"</filter>
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77 </data>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="fastq_input|fastq_input_selector" value="single" />
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82 <param name="fastq_input|fastq_input1" ftype="fastqsanger" value="cd-hit-dup_in.fastqsanger"/>
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83 <output name="output_reads" ftype="fastqsanger" file="cd-hit-dup_out.fastqsanger" />
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84 <output name="output_duplicate_clusters" ftype="tabular" file="cd-hit-dup_out.dup_clusters.tabular" />
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85 </test>
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86 <test>
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87 <param name="fastq_input|fastq_input_selector" value="single" />
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88 <param name="fastq_input|fastq_input1" ftype="fastqsanger" value="cd-hit-dup_in.fastqsanger"/>
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89 <param name="fastq_input|filter_chimeras|filter_chimeras_selector" value="true"/>
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90 <output name="output_reads" ftype="fastqsanger" file="cd-hit-dup_out_chimera.fastqsanger" />
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91 <output name="output_duplicate_clusters" ftype="tabular" file="cd-hit-dup_out_chimera.dup_clusters.tabular" />
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92 <output name="output_chimeric_clusters" ftype="tabular" file="cd-hit-dup_out_chimera.chimeric_clusters.tabular" />
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93 </test>
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94 </tests>
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95 <help>
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96 <![CDATA[
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97 **What it does**
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98
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99 cd-hit-dup is a simple tool for removing duplicates from sequencing reads, with optional step to detect and remove chimeric reads.
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100
1
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101 .. class:: infomark
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102
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103 **TIP:** Chimeric filtering is only available on single-ended, or joined paired-end, reads.
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104
0
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105 **Options**
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106
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107 cd-hit-dup provides a number of options to tune how the duplicates are removed::
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108
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109 -d Description length (default 0, truncate at the first whitespace character)
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110 -u Length of prefix to be used in the analysis (default 0, for full/maximum length)
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111 -m Match length (true/false, default true)
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112 -e Maximum number/percent of mismatches allowed
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113 -f Filter out chimeric clusters (true/false, default false)
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114 -s Minimum length of common sequence shared between a chimeric read and each of
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115 its parents (default 30, minimum 20)
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116 -a Abundance cutoff (default 1 without chimeric filtering, 2 with chimeric filtering)
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117 -b Abundance ratio between a parent read and a chimeric read (default 1)
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118 -p Dissimilarity control for chimeric filtering (default 1)
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119
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120 ]]>
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121 </help>
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122 <citations>
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123 <citation type="doi">10.1093/bioinformatics/bts565</citation>
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124 </citations>
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125 </tool>