Mercurial > repos > iuc > mothur_make_biom

annotate make.biom.xml @ 4:9da0a5f7df8c 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 09:28:29 -0500
parents fe0c38ac3adb
children 063d478e1c94
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48e4f4dcf0ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_make_biom" name="Make.biom" version="@WRAPPER_VERSION@.0">
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2 <description>Make biom files from a shared file</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"/>
1
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9 <command><![CDATA[
4
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10 @SHELL_OPTIONS@
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11
4
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12 ## create symlinks to input datasets
9da0a5f7df8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$otu' otu.dat &&
9da0a5f7df8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$constaxonomy' constaxonomy.dat &&
9da0a5f7df8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 ln -s '$metadata' metadata.dat &&
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16 #if $picrustc.use == "yes":
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17 ln -s '$picrustc.picrust' picrustc.picrust.dat &&
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18 ln -s '$picrustc.reftax' picrustc.reftax.dat &&
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19 #end if
0
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20
4
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21 echo 'make.biom(
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22 shared=otu.dat,
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23 #if $constaxonomy:
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24 constaxonomy=constaxonomy.dat,
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25 #end if
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26 #if $label:
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27 label=${ str($label).replace(",","-") },
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28 #end if
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29 #if $groups:
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30 groups=${ str($groups).replace(",","-") },
9da0a5f7df8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 #end if
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32 #if $metadata:
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33 metadata=metadata.dat,
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34 #end if
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35 #if $picrustc.use == "yes":
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36 picrust=picrustc.picrust.dat,
9da0a5f7df8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 reftaxonomy=picrustc.reftax.dat,
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38 #end if
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39 matrixtype=$matrixtype
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40 )'
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41 | sed 's/ //g' ## mothur trips over whitespace
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42 | mothur
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43 | tee mothur.out.log
0
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44 ]]></command>
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45 <inputs>
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46 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
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47 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="contaxonomy - consensus taxonomy" help="The contaxonomy file is the taxonomy file outputted by classify.otu"/>
4
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48 <param name="metadata" type="data" format="tabular,txt" label="metadata" optional="true" help="You can add sample data support here"/>
0
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49 <conditional name="picrustc">
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50 <param name="use" type="select" label="use picrust program">
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51 <option value="no" selected="true">no</option>
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52 <option value="yes">yes</option>
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53 </param>
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54 <when value="yes">
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55 <param name="picrust" type="data" format="tabular" label="picrust" help="The picrust program requires green genes OTU IDs. The picrust parameter allows you to provide the OTU ID mapping table associated with your reference taxonomy"/>
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56 <param name="reftax" type="data" format="mothur.ref.taxonomy" label="reftaxonomy" help="The referencetax parameter is used with the picrust parameter. Picrust requires the greengenes OTU IDs to be in the biom file, and the referencetax parameter allows you to provide your reference taxonomy file you used when classifying your sequences"/>
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57 </when>
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58 <when value="no"/>
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59 </conditional>
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60 <param name="matrixtype" type="select" label="matrixtype - sparse or dense">
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61 <option value="sparse">sparse</option>
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62 <option value="dense">dense</option>
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63 </param>
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64 <param name="groups" type="select" multiple="true" label="groups - Groups to include" help="By default all are included if no selection is made">
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65 <options>
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66 <filter type="data_meta" ref="otu" key="groups"/>
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67 </options>
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68 </param>
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69 <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels to include" help="By default all are included if no selection is made">
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70 <expand macro="labeloptions"/>
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71 </param>
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72 </inputs>
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73 <outputs>
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74 <expand macro="logfile-output"/>
4
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75 <collection name="biomfiles" type="list" label="${tool.name} on ${on_string}: biom files">
0
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76 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.biom" format="biom1"/>
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77 </collection>
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78 </outputs>
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79 <tests>
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80 <test><!-- test with defaults -->
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81 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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82 <output_collection name="biomfiles" count="36">
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83 <element name="0.36" ftype="biom1">
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84 <assert_contents>
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85 <has_text text="Biological Observation Matrix"/>
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86 <has_text text="generated_by"/>
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87 <has_text text="forest"/>
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88 <has_text text="pasture"/>
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89 </assert_contents>
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90 </element>
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91 </output_collection>
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92 <expand macro="logfile-test"/>
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93 </test>
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94 <test><!-- test with subset of labels and groups-->
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95 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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96 <param name="label" value="0.36,0.38,0.41"/>
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97 <param name="groups" value="forest"/>
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98 <output_collection name="biomfiles" count="3">
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99 <element name="0.36">
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100 <assert_contents>
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101 <has_text text="Biological Observation Matrix"/>
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102 <has_text text="generated_by"/>
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103 <has_text text="forest"/>
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104 <not_has_text text="pasture"/>
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105 </assert_contents>
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106 </element>
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107 </output_collection>
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108 <expand macro="logfile-test"/>
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109 </test>
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110 <test><!-- test with constaxonomy and metadata -->
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111 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
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112 <param name="constaxonomy" value="final.tx.1.cons.taxonomy" ftype="mothur.cons.taxonomy"/>
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113 <param name="metadata" value="metadata"/>
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114 <output_collection name="biomfiles" count="1">
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115 <element name="1" ftype="biom1">
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116 <assert_contents>
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117 <has_text text="Biological Observation Matrix"/>
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118 <has_text text="generated_by"/>
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119 <has_text text="galaxy rocks"/>
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120 </assert_contents>
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121 </element>
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122 </output_collection>
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123 <expand macro="logfile-test"/>
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124 </test>
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125 <!-- TODO: test with picrust option (need file with greengenes OTU IDs) -->
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126 </tests>
4
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127 <help><![CDATA[
0
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128
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129 @MOTHUR_OVERVIEW@
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130
1
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131 **Command Documentation**
0
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132
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133 The make.biom command converts a shared_ shared file to biom_ files.
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134 The output can be filtered by groups and labels.
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135
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136
1
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137 .. _shared: https://www.mothur.org/wiki/Shared_file
0
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138 .. _biom: http://biom-format.org/documentation/biom_format.html
1
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139 .. _make.biom: https://www.mothur.org/wiki/Make.biom
4
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140
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141 ]]></help>
0
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142 <expand macro="citations"/>
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143 </tool>