Mercurial > repos > iuc > mothur_get_sharedseqs

annotate get.sharedseqs.xml @ 3:30f2529d9cc6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:32:40 -0500
parents e4e0bfb92a94
children 779fb6464cd5
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1 <tool profile="16.07" id="mothur_get_sharedseqs" name="Get.sharedseqs" version="@WRAPPER_VERSION@.0">
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2 <description>Get shared sequences at each distance from list and group</description>
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3 <macros>
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4 <import>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><![CDATA[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
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13 ln -s '$infile.otu' infile_otu.dat &&
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14 #if $infile.intype == "in_listgroup":
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15 ln -s '$infile.group' infile.group.dat &&
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16 ln -s '$infile.fasta' infile_fasta.dat &&
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17 ln -s '$count_in' count_in.dat &&
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18 #end if
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19
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20 echo 'get.sharedseqs(
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21 #if $infile.intype == "in_listgroup":
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22 list=infile_otu.dat
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23
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24 #if $group:
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25 ,group=infile.group.dat
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26 #elif $count_in:
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27 ,count=count_in.dat
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28 #end if
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29
3
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30 #if $infile.fasta:
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31 ,fasta=infile_fasta.dat
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32 #end if
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33 #else
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34 shared=infile_otu.dat
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35 #end if
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36 #if $infile.label:
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37 ,label=${ str($infile.label).replace(",","-") }
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38 #end if
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39 #if $infile.seqsfrom.selection == "unique" and $infile.seqsfrom.groups:
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40 ,uniquegroups=${ str($infile.seqsfrom.groups).replace(",","-") }
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41 #end if
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42 #if $infile.seqsfrom.selection == "shared" and $infile.seqsfrom.groups:
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43 ,sharedgroups=${ str($infile.seqsfrom.groups).replace(",","-") }
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44 #end if
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45 #if $output:
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46 ,output=$output
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47 #end if
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48 )'
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49 | sed 's/ //g' ## mothur trips over whitespace
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50 | mothur
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51 | tee mothur.out.log
0
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52 ]]></command>
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53 <inputs>
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54 <conditional name="infile">
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55 <param name="intype" type="select" label="Will you be supplying a shared file or a list and group file?" help="">
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56 <option value="in_shared">Shared file</option>
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57 <option value="in_listgroup">OTU list and group file</option>
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58 </param>
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59 <when value="in_shared">
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60 <param name="otu" type="data" format="mothur.shared" label="list - OTU List or shared file"/>
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61 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
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62 <options>
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63 <filter type="data_meta" ref="otu" key="labels"/>
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64 </options>
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65 </param>
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66 <conditional name="seqsfrom">
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67 <param name="selection" type="select" label="Select Groups" help="">
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68 <option value="all" selected="true">None (use all groups)</option>
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69 <option value="unique">OTUs that contain ONLY sequences from the selected groups</option>
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70 <option value="shared">OTUs that contain sequences from the selected groups</option>
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71 </param>
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72 <when value="unique">
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73 <param name="groups" type="select" multiple="true" label="unique - Group to analyze">
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74 <options>
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75 <filter type="data_meta" ref="otu" key="groups"/>
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76 </options>
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77 </param>
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78 </when>
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79 <when value="shared">
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80 <param name="groups" type="select" multiple="true" label="shared - Groups to analyze">
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81 <options>
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82 <filter type="data_meta" ref="otu" key="groups"/>
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83 </options>
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84 </param>
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85 </when>
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86 <when value="all"/>
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87 </conditional>
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88 </when>
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89 <when value="in_listgroup">
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90 <param name="otu" type="data" format="mothur.list" label="list - OTU List or shared file"/>
3
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91 <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels to include"
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92 help="By default all are included if no selection is made">
0
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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93 <options>
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94 <filter type="data_meta" ref="otu" key="labels"/>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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95 </options>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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96 </param>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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97 <param name="group" type="data" format="mothur.groups" optional="true" label="group - not required if using a shared file"/>
3
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98 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
30f2529d9cc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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99 <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset"
30f2529d9cc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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100 help="will output a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified"/>
0
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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101 <conditional name="seqsfrom">
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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102 <param name="selection" type="select" label="Select Groups" help="">
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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103 <option value="all" selected="true">None (use all groups)</option>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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104 <option value="unique">OTUs that contain ONLY sequences from the selected groups</option>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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105 <option value="shared">OTUs that contain sequences from the selected groups</option>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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106 </param>
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107 <when value="unique">
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108 <param name="groups" type="select" multiple="true" label="unique - Group to analyze">
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109 <options>
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110 <filter type="data_meta" ref="group" key="groups"/>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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111 </options>
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112 </param>
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113 </when>
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114 <when value="shared">
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115 <param name="groups" type="select" multiple="true" label="shared - Groups to analyze">
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116 <options>
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117 <filter type="data_meta" ref="group" key="groups"/>
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118 </options>
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119 </param>
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120 </when>
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121 <when value="all"/>
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122 </conditional>
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123 </when>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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124 </conditional>
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125 <param name="output" type="select" label="output - select the output format" help="accnos can be used with get.seqs, list.seqs and remove.seqs">
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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126 <option value="" selected="true">default: (name group bin_number)</option>
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127 <option value="accnos">accnos (name)</option>
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128 </param>
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129 </inputs>
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130 <outputs>
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131 <expand macro="logfile-output"/>
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132 <collection name="sharedseqs" type="list" label="${tool.name} on ${on_string}: shared.seqs">
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133 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.seqs" format="tabular"/>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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134 <filter>output != 'accnos'</filter>
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135 </collection>
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136 <collection name="sharedaccnos" type="list" label="${tool.name} on ${on_string}: shared.accnos">
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137 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.accnos" format="mothur.accnos"/>
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138 <filter>output == 'accnos'</filter>
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139 </collection>
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140 <collection name="sharedfastas" type="list" label="${tool.name} on ${on_string}: shared.fastas">
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141 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.fasta" format="fasta"/>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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142 <filter>infile['fasta']</filter>
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143 </collection>
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144 </outputs>
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145 <tests>
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146 <test><!-- test with shared file -->
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147 <param name="intype" value="in_shared"/>
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148 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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149 <param name="selection" value="shared"/>
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150 <output_collection name="sharedseqs" count="35">
3
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151 <element name="0.41.unique.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
0
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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152 </output_collection>
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153 <expand macro="logfile-test"/>
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154 </test>
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155 <test><!-- test with list and group file -->
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156 <param name="intype" value="in_listgroup"/>
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157 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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158 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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159 <output_collection name="sharedseqs" count="35">
3
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160 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
0
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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161 </output_collection>
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162 <expand macro="logfile-test"/>
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163 </test>
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164 <test><!-- test with shared seqs and subset of labels -->
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165 <param name="intype" value="in_shared"/>
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166 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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167 <param name="selection" value="shared"/>
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168 <param name="groups" value="forest,pasture"/>
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169 <param name="label" value="0.03,0.33,0.41"/>
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170 <output_collection name="sharedseqs" count="3">
3
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171 <element name="0.41.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
0
d20133cb8909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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172 </output_collection>
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173 <expand macro="logfile-test"/>
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174 </test>
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175 <test><!-- test with unique seqs and subset of groups -->
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176 <param name="intype" value="in_shared"/>
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177 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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178 <param name="selection" value="unique"/>
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179 <param name="groups" value="pasture"/>
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180 <output_collection name="sharedseqs" count="34">
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181 <element name="0.41.unique.pasture" md5="f4735f56d96d13cd603ca0b11c4bc231" ftype="tabular"/>
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182 </output_collection>
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183 <expand macro="logfile-test"/>
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184 </test>
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185 <test><!-- test with accnos output -->
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186 <param name="intype" value="in_shared"/>
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187 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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188 <param name="output" value="accnos"/>
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189 <output_collection name="sharedaccnos" count="35">
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190 <element name="0.41.unique.forest_pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/>
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191 </output_collection>
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192 <expand macro="logfile-test"/>
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193 </test>
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194 <test><!-- test with fasta input and output -->
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195 <param name="intype" value="in_listgroup"/>
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196 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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197 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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198 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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199 <output_collection name="sharedseqs" count="35">
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200 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
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201 </output_collection>
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202 <output_collection name="sharedfastas" count="35">
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203 <element name="0.41.unique.forest_pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/>
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204 </output_collection>
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205 <expand macro="logfile-test"/>
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206 </test>
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207 </tests>
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208 <help><![CDATA[
0
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209
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210 @MOTHUR_OVERVIEW@
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211
1
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212 **Command Documentation**
0
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213
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214 The get.sharedseqs_ command takes a list and group file and outputs a .shared.seqs file for each distance. This is useful for those cases where you might be interested in identifying sequences that are either unique or shared by specific groups, which you could then classify.
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215
1
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216 .. _get.sharedseqs: https://www.mothur.org/wiki/Get.sharedseqs
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217
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218 v1.21.0: Updated to Mothur 1.33, added shared file option
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219
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220 ]]></help>
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221 <expand macro="citations"/>
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222 </tool>