Mercurial > repos > iuc > obi_clean

annotate obiclean.xml @ 6:fea356c8cd06 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit b017355279c18334e66ea8c0c0d7727fbd2876f7
author iuc
date Thu, 13 Nov 2025 10:22:44 +0000
parents c78f86dd30c1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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1 <tool id="obi_clean" name="obiclean" version="@TOOL_VERSION@" profile="@PROFILE@">
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <description>tags a set of sequences for PCR/sequencing errors identification</description>
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
5
c78f86dd30c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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10 <command><![CDATA[
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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11 @GUNZIP_INPUT@
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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12 obiclean
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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13 --without-progress-bar
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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14 #if $distance
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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15 -d '$distance'
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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16 #end if
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17 #if $key
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18 -s '$key'
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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19 #end if
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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20 #if $ratio
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21 -r '$ratio'
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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22 #end if
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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23 ${head}
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24 @INPUT_FORMAT@
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25 @OUT_FORMAT@
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26 input
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27 @GZIP_OUTPUT@
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28 >'$output'
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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29 @GENERATE_GALAXY_JSON@
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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30 ]]></command>
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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31 <inputs>
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32 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
c78f86dd30c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
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33 <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)"/>
c78f86dd30c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
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34 <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition"/>
c78f86dd30c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
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35 <param name="ratio" optional="true" type="float" value="1" label="Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants)"/>
c78f86dd30c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
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36 <param name="head" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Do you want to select only sequences with the head status in a least one sample?"/>
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37 <expand macro="input_format_options_macro"/>
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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38 <expand macro="out_format_macro"/>
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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39 </inputs>
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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40 <outputs>
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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41 <data format="auto" name="output"/>
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42 </outputs>
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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43 <tests>
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44 <test expect_num_outputs="1">
4
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45 <param name="input" value="output_obiannotate.fasta" />
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46 <param name="head" value="True"/>
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47 <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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48 </test>
5
c78f86dd30c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
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49 <test expect_num_outputs="1">
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50 <param name="input" value="output_obiannotate.fasta.gz" />
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51 <param name="key" value="merged_sample"/>
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52 <param name="ratio" value="0.05"/>
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53 <param name="head" value="False"/>
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54 <output name="output" file="output_obiclean_advanced.fasta.gz" ftype="fasta.gz" decompress="true"/>
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55 </test>
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56 </tests>
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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57 <help><![CDATA[
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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58
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59 .. class:: infomark
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60
c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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61 **What it does**
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62
6
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63 obiclean is a command that classifies sequence records either as head, internal or singleton.
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64
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65 For that purpose, two pieces of information are used:
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66
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67 - sequence record counts
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68 - sequence similarities
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69
6
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70 S1 a sequence record is considered as a variant of S2 another sequence record if and only if:
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71
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72 - count of S1 divided by count of S2 is lesser than the ratio R. R default value is set to 1, and can be adjusted between 0 and 1 with the -r option.
fea356c8cd06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit b017355279c18334e66ea8c0c0d7727fbd2876f7
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73 - both sequences are related to one another (they can align with some differences, the maximum number of differences can be specified by the -d option).
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74
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75 Considering S a sequence record, the following properties hold for S tagged as:
4
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76
6
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77 **head:**
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78 - there exists at least one sequence record in the dataset that is a variant of S
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79 - there exists no sequence record in the dataset such that S is a variant of this sequence record
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80
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81 **internal:**
fea356c8cd06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit b017355279c18334e66ea8c0c0d7727fbd2876f7
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82 - there exists at least one sequence record in the dataset such that S is a variant of this sequence record
4
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83
6
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84 **singleton:**
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85 - there exists no sequence record in the dataset that is a variant of S
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86 - there exists no sequence record in the dataset such that S is a variant of this sequence record
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88 By default, tagging is done once for the whole dataset, but it can also be done sample by sample by specifying the -s option. In such a case, the counts are extracted from the sample information.
fea356c8cd06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit b017355279c18334e66ea8c0c0d7727fbd2876f7
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89
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90 Finally, each sequence record is annotated with three new attributes head, internal and singleton. The attribute values are the numbers of samples in which the sequence record has been classified in this manner.
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c210936fafe0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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91
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92 @OBITOOLS_LINK@
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93
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94 ]]>
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95 </help>
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96 <expand macro="citation"/>
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97 </tool>