Mercurial > repos > iuc > mothur_biom_info

annotate biom.info.xml @ 8:458d9a13d2f5 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 11:49:06 +0000
parents c664838f087c
children
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c664838f087c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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1 <tool profile="16.07" id="mothur_biom_info" name="Biom.info" version="@WRAPPER_VERSION@.0">
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2 <description>create shared and taxonomy files from biom</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
8
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command><![CDATA[
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11 @SHELL_OPTIONS@
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12
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13 ln -s '$biom' input.biom &&
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14
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15 echo 'biom.info(
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16 biom=input.biom,
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17 #if str($label) != '':
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18 label=$label,
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19 #end if
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20 basis=$basis,
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21 output=$output,
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22 relabund=$relabund,
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23 printlevel=$printlevel
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24 )'
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25 | sed 's/ //g' ## mothur trips over whitespace
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26 | mothur
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27 | tee mothur.out.log
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28 ]]></command>
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29 <inputs>
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30 <param argument="biom" type="data" format="biom1" label="Biom input dataset"/>
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31 <!-- TODO: read label options from biom file -->
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32 <param argument="label" type="text" value="userLabel" label="label - OTU Labels"
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33 help="Enter a distance label to be used in the shared file created from your biom file (e.g. 0.03)"/>
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34 <param argument="basis" type="select" label="Summary type"
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35 help="indicate what you want the summary file to represent, options are otu and sequence. Default is otu.
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36 For example consider the following basis=sequence could give Clostridiales 3 105, where 105 is the total
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37 number of sequences whose otu classified to Clostridiales. Now for basis=otu could give Clostridiales 3 7,
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38 where 7 is the number of otus that classified to Clostridiales. ">
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39 <option value="otu" selected="true">OTU</option>
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40 <option value="sequence">Sequence</option>
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41 </param>
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42 <param argument="relabund" type="boolean" truevalue="T" falsevalue="F" label="Relative abundance values"
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43 help="use relative abundances rather than raw abundances for the tax.summary file"/>
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44 <expand macro="param-output"/>
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45 <expand macro="param-printlevel"/>
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46 <expand macro="param-savelog"/>
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47 </inputs>
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48 <outputs>
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49 <expand macro="logfile-output"/>
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50 <data name="shared" format="mothur.shared" from_work_dir="input*.shared" label="${tool.name} on ${on_string}: shared"/>
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51 <data name="taxonomy" format="mothur.cons.taxonomy" from_work_dir="input*.cons.taxonomy" label="${tool.name} on ${on_string}: cons.taxonomy"/>
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52 <data name="tax.summary" format="mothur.tax.summary" from_work_dir="input*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
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53 </outputs>
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54 <tests>
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55 <test><!-- test with biom without metadata -->
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56 <param name="biom" value="samplebiom.biom1"/>
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57 <output name="shared" ftype="mothur.shared">
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58 <assert_contents>
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59 <expand macro="test-shared-format"/>
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60 </assert_contents>
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61 </output>
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62 <param name="savelog" value="true"/>
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63 <expand macro="logfile-test"/>
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64 </test>
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65 <test><!-- test with biom file with metadata -->
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66 <param name="biom" value="example.biom"/>
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67 <output name="shared" ftype="mothur.shared">
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68 <assert_contents>
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69 <expand macro="test-shared-format"/>
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70 </assert_contents>
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71 </output>
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72 <output name="taxonomy" ftype="mothur.cons.taxonomy">
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73 <assert_contents>
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74 <expand macro="test-taxonomy-format"/>
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75 <has_text text="GG_OTU_1"/>
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76 </assert_contents>
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77 </output>
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78 <output name="tax.summary" ftype="mothur.tax.summary">
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79 <assert_contents>
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80 <expand macro="test-taxsummary-format"/>
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81 </assert_contents>
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82 </output>
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83 <param name="savelog" value="true"/>
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84 <expand macro="logfile-test"/>
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85 </test>
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86 <test><!-- test with some more parameters -->
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87 <param name="biom" value="example.biom"/>
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88 <param name="label" value="0.03"/>
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89 <param name="output" value="detail"/>
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90 <param name="basis" value="sequence"/>
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91 <param name="printlevel" value="4"/>
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92 <output name="shared" ftype="mothur.shared">
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93 <assert_contents>
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94 <expand macro="test-shared-format"/>
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95 </assert_contents>
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96 </output>
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97 <output name="taxonomy" ftype="mothur.cons.taxonomy">
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98 <assert_contents>
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99 <expand macro="test-taxonomy-format"/>
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100 <has_text text="GG_OTU_1"/>
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101 </assert_contents>
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102 </output>
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103 <output name="tax.summary" ftype="mothur.tax.summary">
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104 <assert_contents>
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105 <expand macro="test-taxsummary-format"/>
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106 <has_text text="Euryarchaeota"/>
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107 </assert_contents>
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108 </output>
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109 <param name="savelog" value="true"/>
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110 <expand macro="logfile-test"/>
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111 </test>
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112 </tests>
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113 <help><![CDATA[
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114
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115 @MOTHUR_OVERVIEW@
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116
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117 **Command Documentation**
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118
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119 The biom.info command reads a biom file creates a shared file. If your biom file contains metadata mothur will also
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120 create taxonomy or constaxonomy along with tax.summary files.
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121
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122 ]]></help>
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123 <expand macro="citations"/>
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124 </tool>