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annotate chimera.xml @ 10:32e8ed5c6100 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb"
author iuc
date Wed, 04 Nov 2020 07:35:42 +0000
parents 50cc0d99b800
children
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50cc0d99b800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit b'29f6e6424a37947adbe1eba92f0e7d3c83efc042'
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1 <tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>vsearch_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11 vsearch
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12 @GENERAL@
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13 --abskew "${abskew}"
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14 --chimeras "${outfile}"
e8401372796a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
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15 --dn "${dn}"
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16 --mindiffs "${mindiffs}"
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17 --mindiv "${mindiv}"
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18 --minh "${minh}"
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19 --xn "${xn}"
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20 $self_param
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21 $selfid_param
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22 #if $detection_mode.detection_mode_select == 'denovo':
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23 --uchime_denovo "${detection_mode.infile_denovo}"
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24 #else:
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25 --uchime_ref $detection_mode.infile_reference
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26 --db "${detection_mode.db}"
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27 #end if
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28
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29 #if 'nonchimeras' in str($outputs).split( "," ):
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30 --nonchimeras "${nonchimeras}"
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31 #end if
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32 #if 'uchimealns' in str($outputs).split( "," ):
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33 --uchimealns "${uchimealns}"
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34 #end if
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35 #if 'uchimeout' in str($outputs).split( "," ):
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36 --uchimeout "${uchimeout}"
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37 #end if
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38
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39 ]]>
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40 </command>
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41 <inputs>
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42 <conditional name="detection_mode">
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43 <param name="detection_mode_select" type="select" label="Detect chimeras" help="">
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44 <option value="denovo">de novo</option>
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45 <option value="reference">using a reference database</option>
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46 </param>
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47 <when value="denovo">
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48 <param name="infile_denovo" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_denovo)" />
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49 </when>
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50 <when value="reference">
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51 <param name="infile_reference" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_ref)" />
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52 <param name="db" type="data" format="fasta" label="Select your reference database" help="(--db)" />
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53 </when>
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54 </conditional>
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55
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56 <param name="abskew" type="float" value="2.0" label="Minimal abundance ratio of parent vs chimera"
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57 help="(--abskew)"/>
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58 <param name="dn" type="float" value="1.4" label="'no' vote pseudo count"
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59 help="(--dn)"/>
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60 <param name="xn" type="float" value="8.0" label="'no' vote weight"
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61 help="(--xn)"/>
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62 <param name="mindiffs" type="integer" value="3" label="Minimum number of differences in segment"
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63 help="(--mindiffs)"/>
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64 <param name="mindiv" type="float" value="0.8" label="Minimum divergence from closest parent"
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65 help="(--mindiv)"/>
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66 <param name="minh" type="float" value="0.28" label="Minimum score"
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67 help="(--minh)"/>
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68
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69 <expand macro="self_and_selfid" />
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71 <param name="outputs" type="select" multiple="True" optional="True"
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72 label="Select output formats" help="(--qmask)">
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73 <option value="nonchimeras">Non-chimeric sequences (--nonchimeras)</option>
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74 <option value="uchimealns">Chimera alignments (--uchimealns)</option>
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75 <option value="uchimeout">Chimera info to tab-separated (--uchimeout)</option>
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76 </param>
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77
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78 </inputs>
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79 <outputs>
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80 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
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81 <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera">
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82 <filter>outputs and 'nonchimeras' in outputs</filter>
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83 </data>
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84 <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments">
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85 <filter>outputs and 'uchimealns' in outputs</filter>
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86 </data>
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87 <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information">
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88 <filter>outputs and 'uchimeout' in outputs</filter>
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89 </data>
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="detection_mode_select" value="denovo"/>
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94 <param name="infile_denovo" value="PR2-18S-rRNA-V4.derep.fsa.bz2" ftype="fasta" />
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95 <param name="outputs" value="uchimeout"/>
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96 <output name="outfile" file="chimera_result1.fasta" ftype="fasta" />
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97 <output name="uchimeout" file="chimera_uchimeout_result1.tabular" ftype="tabular" />
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98 </test>
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99 </tests>
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100 <help>
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101 <![CDATA[
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102 **What it does**
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103
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104 Sequence chimera detection based on a different scoring functions.
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105
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106 Chimera detection options
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107 --abskew REAL min abundance ratio of parent vs chimera (2.0)
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108 --alignwidth INT width of alignment in uchimealn output (80)
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109 --chimeras FILENAME output chimeric sequences to file
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110 --db FILENAME reference database for --uchime_ref
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111 --dn REAL 'no' vote pseudo-count (1.4)
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112 --mindiffs INT minimum number of differences in segment (3)
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113 --mindiv REAL minimum divergence from closest parent (0.8)
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114 --minh REAL minimum score (0.28)
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115 --nonchimeras FILENAME output non-chimeric sequences to file
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116 --self exclude identical labels for --uchime_ref
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117 --selfid exclude identical sequences for --uchime_ref
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118 --uchime_denovo FILENAME detect chimeras de novo
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119 --uchime_ref FILENAME detect chimeras using a reference database
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120 --uchimealns FILENAME output chimera alignments to file
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121 --uchimeout FILENAME output to chimera info to tab-separated file
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122 --uchimeout5 make output compatible with uchime version 5
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123 --xn REAL 'no' vote weight (8.0)
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124
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125 @EXTERNAL_DOCUMENTATION@
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126
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127
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128 ]]>
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129 </help>
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130 <expand macro="citations" />
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131 </tool>