Mercurial > repos > iuc > mothur_get_groups

annotate get.groups.xml @ 3:df59638b9be8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author iuc
date Fri, 06 Apr 2018 04:20:25 -0400
parents 1715be05e718
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e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_get_groups" name="Get.groups" version="@WRAPPER_VERSION@.0">
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2 <description>Select 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[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$group_in' group_in.dat &&
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14 ln -s '$fasta_in' fasta_in.dat &&
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15 ln -s '$name_in' name_in.dat &&
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16 ln -s '$list_in' list_in.dat &&
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17 ln -s '$shared_in' shared_in.dat &&
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18 ln -s '$taxonomy_in' taxonomy_in.dat &&
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19 ln -s '$design_in' design_in.dat &&
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20 ln -s '$column_in' column_in.dat &&
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21 ln -s '$phylip_in' phylip_in.dat &&
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22 #if $groupnames.source == 'accnos':
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23 ln -s '$groupnames.accnos' groupnames.accnos.dat &&
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24 #end if
0
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25
2
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26 echo 'get.groups(
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27 #if $group_in.is_of_type("mothur.groups"):
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28 group=group_in.dat
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29 #else
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30 count=group_in.dat
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31 #end if
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32 #if $groupnames.source == 'groups':
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33 #if $groupnames.groups:
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34 ,groups=${ str($groupnames.groups).replace(",","-") }
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35 #end if
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36 #else
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37 ,accnos=groupnames.accnos.dat
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38 #end if
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39 #if $fasta_in:
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40 ,fasta=fasta_in.dat
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41 #end if
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42 #if $name_in:
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43 ,name=name_in.dat
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44 #end if
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45 #if $list_in:
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46 ,list=list_in.dat
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47 #end if
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48 #if $shared_in:
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49 ,shared=shared_in.dat
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50 #end if
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51 #if $taxonomy_in:
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52 ,taxonomy=taxonomy_in.dat
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53 #end if
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54 #if $design_in:
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55 ,design=design_in.dat
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56 #end if
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57 #if $column_in:
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58 ,column=column_in.dat
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59 #end if
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60 #if $phylip_in:
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61 ,phylip=phylip_in.dat
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62 #end if
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63 )'
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64 | sed 's/ //g' ## mothur trips over whitespace
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65 | mothur
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66 | tee mothur.out.log
0
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67 ]]></command>
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68 <inputs>
2
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69 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" optional="true" label="group or count_table file"/>
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70 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
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71 <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping"
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72 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
0
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73 <conditional name="groupnames">
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74 <param name="source" type="select" label="Select Group Names from">
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75 <option value="groups">A List of Group Names</option>
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76 <option value="accnos">A History Group Name Accnos Dataset</option>
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77 </param>
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78 <when value="groups">
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79 <param name="groups" type="select" multiple="true" label="groups - Pick groups to include">
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80 <options>
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81 <filter type="data_meta" ref="group_in" key="groups"/>
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82 </options>
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83 </param>
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84 </when>
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85 <when value="accnos">
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86 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/>
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87 </when>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 </conditional>
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89 <param name="fasta_in" type="data" format="fasta,mothur.align" optional="true" label="fasta - Fasta Sequences"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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92 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
2
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93 <param name="phylip_in" type="data" format="mothur.lower.dist,mothur.square.dist" optional="true" label="phylip - Distance Matrix you would like to select distances from"
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94 help="must be a phylip-formatted distance matrix"/>
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95 <param name="column_in" type="data" format="mothur.pair.dist" optional="true" label="column - Distance Matrix you would like to select distances from"
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96 help="must be a column-formatted distance matrix"/>
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97 <expand macro="param-savelog"/>
0
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98 </inputs>
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99 <outputs>
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100 <expand macro="logfile-output"/>
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101 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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102 <filter>group_in.ext == "mothur.groups"</filter>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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103 </data>
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104 <data name="count_out" format="mothur.count_table" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.count_table">
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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105 <filter>group_in.ext == "mothur.count_table"</filter>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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106 </data>
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107 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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108 <filter>fasta_in</filter>
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109 </data>
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110 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name">
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111 <filter>name_in</filter>
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112 </data>
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113 <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: pick.list">
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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114 <filter>list_in</filter>
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115 <discover_datasets pattern="list_in.*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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116 </collection>
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117 <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: pick.shared">
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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118 <filter>shared_in</filter>
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119 <discover_datasets pattern="shared_in.*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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120 </collection>
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121 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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122 <filter>taxonomy_in</filter>
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123 </data>
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124 <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design">
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125 <filter>design_in</filter>
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126 </data>
2
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127 <data name="phylip_out" format_source="phylip_in" from_work_dir="phylip_in*.pick.*" label="${tool.name} on ${on_string}: pick.phylip">
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128 <filter>phylip_in</filter>
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129 </data>
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130 <data name="column_out" format="mothur.pair.dist" from_work_dir="column_in*.pick.*" label="${tool.name} on ${on_string}: pick.column">
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131 <filter>column_in</filter>
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132 </data>
0
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133 </outputs>
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134 <tests>
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135 <test><!-- test with group file -->
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136 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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137 <param name="source" value="groups"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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138 <param name="groups" value="forest,pasture"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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139 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
2
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140 <param name="savelog" value="true"/>
0
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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141 <expand macro="logfile-test"/>
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142 </test>
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143 <test><!-- test with accnos file -->
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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144 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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145 <param name="source" value="accnos"/>
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146 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
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147 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
2
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148 <param name="savelog" value="true"/>
0
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149 <expand macro="logfile-test"/>
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150 </test>
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151 <test><!-- test with accnos file and most extra files-->
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152 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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153 <param name="source" value="accnos"/>
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154 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
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155 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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156 <param name="name_in" value="amazon1.names" ftype="mothur.names"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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157 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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158 <param name="shared_in" value="amazon.an.shared" ftype="mothur.shared"/>
e2b43f377f7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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159 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
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160 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
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161 <output name="name_out" md5="1f0324a017e1b71e6ed0af257b0013f3" ftype="mothur.names"/>
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162 <output_collection name="listfiles" count="36">
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163 <element name="0.38" md5="49878dfbe53d5144f3bd885c629de822" ftype="mothur.list"/>
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164 </output_collection>
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165 <output_collection name="sharedfiles" count="36">
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166 <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/>
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167 </output_collection>
2
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168 <param name="savelog" value="true"/>
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169 <expand macro="logfile-test"/>
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170 </test>
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171 <test><!-- test with distance matrix -->
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172 <param name="group_in" value="amazon_withgroups.count_table" ftype="mothur.count_table"/>
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173 <param name="source" value="accnos"/>
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174 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
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175 <param name="column_in" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
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176 <param name="phylip_in" value="amazon.dist" ftype="mothur.square.dist"/>
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177 <output name="column_out" ftype="mothur.pair.dist">
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178 <assert_contents>
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179 <expand macro="test-column-format"/>
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180 <has_text text="U68589"/>
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181 </assert_contents>
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182 </output>
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183 <output name="phylip_out" ftype="mothur.square.dist">
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184 <assert_contents>
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185 <expand macro="test-dist-format"/>
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186 <has_text text="U68589"/>
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187 </assert_contents>
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188 </output>
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189 <param name="savelog" value="true"/>
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190 <expand macro="logfile-test"/>
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191 </test>
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192 </tests>
2
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193 <help><![CDATA[
0
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194
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195 @MOTHUR_OVERVIEW@
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196
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197
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198 **Command Documentation**
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199
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200 The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, fasta, name_, group_, list_, taxonomy_.
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201
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202 .. _name: https://www.mothur.org/wiki/Name_file
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203 .. _group: https://www.mothur.org/wiki/Group_file
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204 .. _list: https://www.mothur.org/wiki/List_file
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205 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
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206 .. _get.groups: https://www.mothur.org/wiki/Get.groups
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207
2
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208 ]]></help>
0
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209 <expand macro="citations"/>
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210 </tool>