Mercurial > repos > iuc > mothur_summary_tax

annotate summary.tax.xml @ 3:f120396eb460 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 04:31:30 -0400
parents f7dded265782
children
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1 <tool profile="16.07" id="mothur_summary_tax" name="Summary.tax" version="@WRAPPER_VERSION@.0">
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2 <description>Assign sequences to taxonomy</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 '$tax.taxonomy' tax.taxonomy.dat &&
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14 ln -s '$name' name.dat &&
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15 ln -s '$group' group.dat &&
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16 ln -s '$count' count.dat &&
0
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17
2
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18 echo 'summary.tax(
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19 taxonomy=tax.taxonomy.dat,
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20 #if $name:
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21 name=name.dat,
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22 #end if
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23 #if $group:
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24 group=group.dat,
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25 #end if
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26 #if $count:
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27 count=count.dat,
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28 #end if
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29 relabund=$relabund,
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30 threshold=$threshold,
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31 output=$output,
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32 printlevel=$printlevel
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33 )'
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34 | sed 's/ //g' ## mothur trips over whitespace
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35 | mothur
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36 | tee mothur.out.log
0
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37 ]]></command>
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38 <inputs>
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39 <conditional name="tax">
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40 <param name="source" type="select" label="Select Taxonomy from" help="">
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41 <option value="hist">History</option>
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42 <option value="ref">Cached Reference</option>
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43 </param>
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44 <when value="ref">
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45 <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference">
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46 <options from_data_table="mothur_taxonomy"/>
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47 </param>
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48 </when>
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49 <when value="hist">
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50 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
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51 </when>
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52 </conditional>
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53 <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
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54 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
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55 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
2
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56 <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false"
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57 label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/>
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58 <param name="threshold" type="integer" value="0" min="0" label="threshold- specify a cutoff for the taxonomy file"
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59 help="Once the classification falls below the threshold the mothur will refer to it as unclassified when calculating the concensus.
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60 This feature is similar to adjusting the cutoff in classify.seqs"/>
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61 <expand macro="param-output"/>
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62 <expand macro="param-printlevel"/>
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63 <expand macro="param-savelog"/>
0
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64 </inputs>
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65 <outputs>
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66 <expand macro="logfile-output"/>
2
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67 <data name="taxsummary" format="mothur.tax.summary" from_work_dir="tax.taxonomy*.tax.summary" label="${tool.name} on ${on_string}: summary"/>
0
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="source" value="hist"/>
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72 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
2
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73 <output name="taxsummary" ftype="mothur.tax.summary">
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74 <assert_contents>
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75 <expand macro="test-taxsummary-format"/>
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76 <has_text text="Root"/>
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77 <has_text text="Bifidobacterium"/>
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78 </assert_contents>
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79 </output>
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80 <param name="savelog" value="true"/>
0
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81 <expand macro="logfile-test"/>
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82 </test>
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83 <test>
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84 <param name="source" value="hist"/>
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85 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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86 <output name="taxsummary" ftype="mothur.tax.summary">
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87 <assert_contents>
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88 <expand macro="test-taxsummary-format"/>
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89 <has_text text="Root"/>
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90 <has_text text="Bifidobacterium"/>
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91 </assert_contents>
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92 </output>
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93 <param name="savelog" value="true"/>
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94 <expand macro="logfile-test"/>
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95 </test>
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96 </tests>
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97 <help><![CDATA[
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98
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99 @MOTHUR_OVERVIEW@
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100
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101 **Command Documentation**
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102
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103 The summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information.
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104
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105 .. _summary.tax: https://www.mothur.org/wiki/Summary.tax
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106
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107 ]]></help>
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108 <expand macro="citations"/>
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109 </tool>