Mercurial > repos > iuc > mothur_get_otus

annotate get.otus.xml @ 3:73f7faafd5ee 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 09:19:54 -0500
parents 054caee6f6e8
children 1a1ab2e282fa
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1 <tool profile="16.07" id="mothur_get_otus" name="Get.otus" version="@WRAPPER_VERSION@.0">
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2 <description>Get otus containing sequences from specified groups</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 '$accnos' accnos.dat &&
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14 #if $list:
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15 ln -s '$list' list.dat &&
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16 #end if
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17 #if $shared:
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18 ln -s '$shared' shared.dat &&
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19 #end if
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20 #if $constaxonomy:
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21 ln -s '$constaxonomy' constaxonomy.dat &&
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22 #end if
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23 #if $corraxes:
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24 ln -s '$corraxes' corraxes.dat &&
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25 #end if
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26 #if $otucorr:
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27 ln -s '$otucorr' otucorr.dat &&
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28 #end if
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29
3
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30 echo 'get.otus(
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31 #if $list
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32 list=list.dat,
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33 #end if
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34 #if $shared
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35 shared=shared.dat,
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36 #end if
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37 #if $corraxes:
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38 corraxes=corraxes.dat,
73f7faafd5ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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39 #end if
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40 #if $otucorr:
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41 otucorr=otucorr.dat,
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42 #end if
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43 #if $constaxonomy
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44 constaxonomy=constaxonomy.dat,
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45 #end if
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46 accnos=accnos.dat
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47 #if $labelsource.label:
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48 ,label=${ str($labelsource.label).replace(",","-") }
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49 #end if
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50 )'
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51 | sed 's/ //g' ## mothur trips over whitespace
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52 | mothur
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53 | tee mothur.out.log
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54 ]]></command>
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55 <inputs>
3
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56 <param argument="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/>
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57 <param argument="list" type="data" format="mothur.list" optional="true" label="OTU List"/>
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58 <param argument="shared" type="data" format="mothur.shared" optional="true" label="OTU List OTU Shared file"/>
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59 <param argument="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="contaxonomy - consensus taxonomy"
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60 help="The contaxonomy file is the taxonomy file outputted by classify.otu"/>
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61 <param argument="otucorr" type="data" format="mothur.otu.corr" optional="true" label="OTU correlation file"
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62 help="otu correlation coefficients are output by the otu.association command"/>
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63 <param argument="corraxes" type="data" format="mothur.axes" optional="true" label="Correlation axes file"
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64 help="correlation axes file is output by the corr.axes command"/>
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65
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66 <conditional name="labelsource">
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67 <param name="source" type="select" label="Select a label from">
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68 <option value="list"> OTU list file </option>
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69 <option value="shared"> OTU shared file </option>
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70 </param>
3
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71 <when value="list">
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72 <param argument="label" type="select" optional="true" multiple="false" label="label - OTU Label"
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73 help="select exactly one label. If none selected, the first label in your file will be used">
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74 <options>
3
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75 <filter type="data_meta" ref="list" key="labels"/>
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76 </options>
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77 </param>
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78 </when>
3
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79 <when value="shared">
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80 <param argument="label" type="select" optional="true" multiple="false" label="label - OTU Label"
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81 help="select exactly one label. If none selected, the first label in your file will be used">
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82 <options>
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83 <filter type="data_meta" ref="shared" key="labels"/>
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84 </options>
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85 </param>
0
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86 </when>
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87 </conditional>
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88 </inputs>
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89 <outputs>
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90 <expand macro="logfile-output"/>
3
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91 <data name="list_out" format="mothur.list" from_work_dir="list*.pick.*" label="${tool.name} on ${on_string}: pick.list">
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92 <filter> $list </filter>
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93 </data>
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94 <data name="shared_out" format="mothur.shared" from_work_dir="shared*.pick.*" label="${tool.name} on ${on_string}: pick.shared">
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95 <filter> $shared </filter>
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96 </data>
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97 <data name="constaxonomy_out" format="mothur.cons.taxonomy" from_work_dir="constaxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.cons.taxonomy">
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98 <filter> $constaxonomy </filter>
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99 </data>
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100 <data name="otucorr_out" format="mothur.otu.corr" from_work_dir="otucorr*.pick.*" label="${tool.name} on ${on_string}: pick.otu.corr">
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101 <filter> $otucorr </filter>
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102 </data>
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103 <data name="corraxes_out" format="mothur.axes" from_work_dir="corraxes*.pick.*" label="${tool.name} on ${on_string}: pick.axes">
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104 <filter> $corraxes </filter>
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105 </data>
0
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106 </outputs>
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107 <tests>
3
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108 <test><!-- test with list file input and default settings -->
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109 <param name="list" value="amazon.an.list" ftype="mothur.list"/>
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110 <param name="accnos" value="amazon.otus.accnos" ftype="mothur.accnos"/>
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111 <output name="list_out" ftype="mothur.list">
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112 <assert_contents>
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113 <expand macro="test-list-format"/>
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114 <has_text text="unique"/>
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115 <has_text text="Otu01"/>
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116 <has_text text="Otu17"/>
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117 <has_text text="Otu42"/>
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118 <not_has_text text="Otu43"/>
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119 </assert_contents>
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120 </output>
0
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121 <expand macro="logfile-test"/>
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122 </test>
3
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123 <test><!-- test with shared and otu.corr file and label select -->
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124 <param name="shared" value="amazon.an.shared" ftype="mothur.shared"/>
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125 <param name="accnos" value="amazon.otus.accnos" ftype="mothur.accnos"/>
0
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126 <param name="label" value="0.03"/>
3
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127 <param name="source" value="shared"/>
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128 <param name="otucorr" value="amazon.an.0.03.pearson.otu.corr" ftype="mothur.cons.taxonomy"/>
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129 <output name="shared_out" ftype="mothur.shared">
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130 <assert_contents>
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131 <expand macro="test-shared-format"/>
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132 <has_text text="0.03"/>
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133 <has_text text="Otu01"/>
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134 <has_text text="Otu17"/>
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135 <has_text text="Otu42"/>
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136 <not_has_text text="Otu43"/>
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137 </assert_contents>
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138 </output>
0
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139 <expand macro="logfile-test"/>
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140 </test>
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141 </tests>
3
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142 <help><![CDATA[
0
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143
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144 @MOTHUR_OVERVIEW@
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145
1
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146 **Command Documentation**
0
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147
3
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148 The get.otus command selects otus from a given list.
0
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149
1
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150 .. _list: https://www.mothur.org/wiki/List_file
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151 .. _get.otus: https://www.mothur.org/wiki/Get.otus
0
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152
3
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153 ]]></help>
0
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154 <expand macro="citations"/>
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155 </tool>