Mercurial > repos > iuc > mothur_chimera_vsearch

annotate chimera.vsearch.xml @ 8:bdb4a58a2025 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 12:12:54 +0000
parents de3cfb122105
children
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de3cfb122105 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
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1 <tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.2">
0
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2 <description>find potential chimeric sequences using vsearch</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
8
bdb4a58a2025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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6 <expand macro="biotools"/>
0
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7 <expand macro="requirements">
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8 <requirement type="package" version="2.6.0">vsearch</requirement>
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9 </expand>
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10 <expand macro="stdio"/>
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11 <expand macro="version_command"/>
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12 <command><![CDATA[
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13 @SHELL_OPTIONS@
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14
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15 ## create symlinks to input datasets
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16 ln -s '$fasta' fasta.dat &&
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17 #if $template.source == "self":
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18 ln -s '$template.count' template.count.dat &&
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19 ln -s '$template.group' template.group.dat &&
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20 #elif $template.source == "names":
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21 ln -s '$template.name' template.name.dat &&
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22 #else:
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23 ln -s '$template.reference' template.reference.dat &&
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24 #end if
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25
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26 echo 'chimera.vsearch(
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27 fasta=fasta.dat,
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28 #if $template.source == "self":
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29 reference=self,
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30 #if float($template.abskew) > 0:
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31 abskew=$template.abskew,
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32 #end if
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33 #if $template.group:
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34 group=template.group.dat,
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35 #end if
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36 #if $template.count:
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37 count=template.count.dat,
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38 #end if
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39 #elif $template.source == "names":
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40 name=template.name.dat,
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41 #else:
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42 reference=template.reference.dat,
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43 #end if
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44 minh=$minh,
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45 mindiv=$mindiv,
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46 xn=$xn,
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47 dn=$dn,
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48 dereplicate=$dereplicate,
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49 mindiffs=$mindiffs,
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50 processors='\${GALAXY_SLOTS:-8}'
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51 )'
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52 | sed 's/ //g' ## mothur trips over whitespace
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53 | mothur
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54 | tee mothur.out.log
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55 2>&1 ## uchime component writes output to stderr
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56 && cat *accnos
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57 ]]></command>
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58 <inputs>
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59 <param argument="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Aligned Sequences"/>
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60 <conditional name="template">
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61 <param name="source" type="select" label="Select Reference Template from">
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62 <option value="hist">History</option>
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63 <option value="ref">Cached Reference</option>
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64 <option value="self">Self</option>
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65 <option value="names">Use a names file</option>
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66 </param>
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67 <when value="ref">
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68 <param argument="reference" type="select" label="reference - Select an alignment database">
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69 <options from_data_table="mothur_aligndb"/>
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70 </param>
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71 </when>
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72 <when value="hist">
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73 <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
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74 </when>
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75 <when value="self">
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76 <param argument="abskew" type="float" value="1.9" label="abskew - Abundance skew" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query). Default 1.9"/>
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77 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"
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78 help="use the more abundant sequences from the same sample to check the query sequence"/>
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79 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table"
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80 help="Generated by count.seqs. When you use a count file with group info and dereplicate=T, mothur will create a count table containing seqeunces after chimeras are removed."/>
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81 </when>
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82 <when value="names">
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83 <param argument="name" type="data" format="mothur.names" label="name - Sequence names"/>
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84 </when>
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85 </conditional>
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86 <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false"
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87 label="dereplicate - remove chimeric sequences from all groups?"
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88 help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/>
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89 <param argument="minh" type="float" value="0.3" min="0" label="minh - mininum score to report chimera. Default 0.3"
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90 help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/>
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91 <param argument="mindiv" type="float" value="0.5" min="0" label="mindiv - minimum divergence ratio"
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92 help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1. Default 0.5"/>
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93 <param argument="xn" type="float" value="8.0" min="0" label="xn - weight of a no vote. Default 8.0"
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94 help="Decreasing this weight to around 3 or 4 may give better performance on denoised data"/>
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95 <param argument="dn" type="float" value="1.4" min="0" label="dn - pseudo-count prior on number of no votes"
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96 help="Reasonable values are probably in the range from 0.2 to 2.0. Default 1.4"/>
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97 <param argument="mindiffs" type="integer" value="3" min="0" label="minimum number of differences in segment"/>
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98 <expand macro="param-savelog"/>
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99 </inputs>
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100 <outputs>
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101 <expand macro="logfile-output"/>
1
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102 <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: vsearch.chimeras"/>
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103 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: vsearch.accnos"/>
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104 <data name="out_count" format="mothur.count_table" from_work_dir="template.*vsearch.pick.count_table" label="${tool.name} on ${on_string}: vsearch.count_table">
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105 <filter>template['source'] == 'self' and template['count'] and template['count'].metadata.groups != []</filter>
1
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106 </data>
0
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107 </outputs>
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108 <tests>
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109 <test expect_num_outputs="3"><!-- de novo test with name file -->
0
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110 <param name="fasta" value="stool_small.unique.fasta"/>
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111 <param name="source" value="names"/>
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112 <param name="name" value="stool_small.names"/>
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113 <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
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114 <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
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115 <param name="savelog" value="true"/>
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116 <expand macro="logfile-test"/>
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117 </test>
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118 <test expect_num_outputs="4"><!-- de novo test with count table-->
1
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119 <param name="fasta" value="chimera.fasta"/>
0
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120 <param name="source" value="self"/>
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121 <param name="count" value="chimera.count_table" ftype="mothur.count_table"/>
1
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122 <param name="dereplicate" value="true"/>
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123 <output name="vsearch.chimeras" file="chimera.vsearch.chimeras" ftype="txt"/>
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124 <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/>
1
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125 <output name="out_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/>
0
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126 <param name="savelog" value="true"/>
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127 <expand macro="logfile-test"/>
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128 </test>
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129 <test expect_num_outputs="3"><!-- de novo test with count table (missing group info)-->
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130 <param name="fasta" value="chimera.fasta"/>
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131 <param name="source" value="self"/>
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132 <param name="count" value="chimera.count_table_wogroups" ftype="mothur.count_table"/>
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133 <param name="dereplicate" value="true"/>
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134 <!-- for some reason only for count tables wo group info header is printed -->
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135 <output name="vsearch.chimeras" file="chimera.vsearch.chimeras_wogroups" ftype="txt"/>
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136 <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/>
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137 <param name="savelog" value="true"/>
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138 <expand macro="logfile-test"/>
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139 </test>
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140 <test expect_num_outputs="3"><!-- test with reference file -->
0
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141 <param name="fasta" value="stool_small.unique.fasta"/>
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142 <param name="source" value="hist"/>
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143 <param name="reference" value="stool_small.unique.fasta"/>
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144 <output name="vsearch.chimeras" ftype="txt">
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145 <assert_contents>
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146 <expand macro="test-chimera-format"/>
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147 <has_text text="F11Fcsw_12747"/>
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148 </assert_contents>
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149 </output>
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150 <output name="out_accnos" ftype="mothur.accnos">
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151 <assert_contents>
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152 <expand macro="test-accnos-format"/>
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153 <has_text text="F11Fcsw_23322"/>
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154 </assert_contents>
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155 </output>
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156 <param name="savelog" value="true"/>
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157 <expand macro="logfile-test"/>
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158 </test>
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159 </tests>
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160 <help><![CDATA[
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161
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162 @MOTHUR_OVERVIEW@
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163
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164 **Command Documentation**
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165
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166 The chimera.vsearch_ command reads a fasta file and reference file and outputs potentially chimeric sequences.
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167
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168 .. _chimera.vsearch: https://www.mothur.org/wiki/Chimera.vsearch
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169
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170 ]]></help>
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171 <expand macro="citations"/>
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172 </tool>