Mercurial > repos > iuc > mothur_summary_tax

annotate summary.tax.xml @ 1:807ebe300c84 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author iuc
date Tue, 05 Sep 2017 16:54:59 -0400
parents 76c27b0fa016
children f7dded265782
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76c27b0fa016 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_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[
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10 @SHELL_OPTIONS@
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11
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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 &&
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17 #if $reftax.source2:
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18 ln -s "$reftax.reftaxonomy" myreftax.taxonomy &&
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19 ln -s "$sum" myreftax.tree.sum &&
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20 #end if
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21
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22 echo 'summary.tax(
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23 taxonomy=tax.taxonomy.dat,
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24 #if $name:
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25 name=name.dat,
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26 #end if
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27 #if $group:
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28 group=group.dat,
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29 #end if
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30 #if $reftax.source2:
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31 reftaxonomy=myreftax.taxonomy,
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32 #end if
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33 #if $count:
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34 count=count.dat,
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35 #end if
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36 relabund=$relabund
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37 )'
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38 | sed 's/ //g' ## mothur trips over whitespace
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39 | mothur
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40 | tee mothur.out.log
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41 ]]></command>
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42 <inputs>
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43 <conditional name="tax">
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44 <param name="source" type="select" label="Select Taxonomy from" help="">
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45 <option value="hist">History</option>
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46 <option value="ref">Cached Reference</option>
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47 </param>
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48 <when value="ref">
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49 <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference">
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50 <options from_data_table="mothur_taxonomy"/>
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51 </param>
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52 </when>
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53 <when value="hist">
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54 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
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55 </when>
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56 </conditional>
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57 <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
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58 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
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59 <conditional name="reftax">
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60 <param name="source2" type="select" label="Select Reference Taxonomy used in Summary.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
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61 <option value="" selected="true">Selection is Optional</option>
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62 <option value="hist">History</option>
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63 <option value="ref">Cached Reference</option>
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64 </param>
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65 <when value="ref">
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66 <param name="reftaxonomy" type="select" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
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67 <options from_data_table="mothur_taxonomy"/>
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68 </param>
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69 <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
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70 </when>
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71 <when value="hist">
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72 <param name="reftaxonomy" type="data" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
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73 <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
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74 </when>
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75 <when value=""/>
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76 </conditional>
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77 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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78 <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" 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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79 </inputs>
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80 <outputs>
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81 <expand macro="logfile-output"/>
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82 <data name="taxsummary" format="mothur.summary" from_work_dir="tax.taxonomy*.tax.summary" label="${tool.name} on ${on_string}: summary"/>
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83 </outputs>
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84 <tests>
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85 <test>
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86 <param name="source" value="hist"/>
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87 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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88 <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/>
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89 <expand macro="logfile-test"/>
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90 </test>
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91 <test>
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92 <param name="source" value="hist"/>
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93 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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94 <param name="source2" value="hist"/>
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95 <param name="reftaxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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96 <param name="sum" value="abrecovery.pds.wang.tree.sum"/>
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97 <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/>
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98 <expand macro="logfile-test"/>
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99 </test>
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100 </tests>
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101 <help>
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102 <![CDATA[
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103
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104 @MOTHUR_OVERVIEW@
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105
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106 **Command Documentation**
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107
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108 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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109
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110 .. _summary.tax: https://www.mothur.org/wiki/Summary.tax
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111 ]]>
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112 </help>
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113 <expand macro="citations"/>
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114 </tool>