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annotate alpha_rarefaction.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="qiime_alpha_rarefaction" name="Perform alpha rarefaction" version="1.9.1">
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2
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3 <description></description>
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4
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements" />
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11 <version_command><![CDATA[
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12 alpha_rarefaction.py --version
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13 ]]>
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14 </version_command>
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16 <command>
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17 <![CDATA[
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18 alpha_rarefaction.py
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19 -i $otu_table_fp
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20 -m $mapping_fp
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21 -o alpha_rarefaction
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22
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23 #if $parameter_fp
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24 -p $parameter_fp
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25 #end if
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26
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27 -n $num_steps
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28 $parallel
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29 -O "\${GALAXY_SLOTS:-4}"
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30
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31 #if $tree_fp
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32 -t $tree_fp
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33 #end if
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34
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35 --min_rare_depth $min_rare_depth
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36
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37 #if $max_rare_depth
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38 -e $max_rare_depth
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39 #end if
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40
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41 &&
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42 mkdir -p $alpha_rarefaction_plots.files_path
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43 &&
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44 cp -r alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots.files_path
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45 &&
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46 cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path
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47 &&
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48 mv $alpha_rarefaction_plots.files_path/rarefaction_plots.html $alpha_rarefaction_plots
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49 ]]>
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50 </command>
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51
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52 <inputs>
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53 <param name="otu_table_fp" type="data" format="tabular,txt,tsv,biom"
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54 label="OTU table" help="(-i/--otu_table_fp)" />
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55
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56 <param name="mapping_fp" type="data" format="tabular,txt,tsv"
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57 label="Mapping file" help="(-m/--mapping_fp)" />
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58
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59 <param name="parameter_fp" type="data" format="txt"
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60 label="Parameter file" help="It specifies changes to the default
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61 behavior (-p/--parameter_fp)" optional="true"/>
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62
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63 <param name="num_steps" type="integer" value="10" label="Number of steps
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64 (or rarefied OTU table sizes) to make between min and max counts"
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65 help="(-n/--num_steps)"/>
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66
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67 <param name="parallel" type="boolean" label="Run in parallel where
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68 available?" truevalue="--parallel" falsevalue="" checked="True"
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69 help="(-a, --parallel)" />
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70
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71 <param name="tree_fp" type="data" format="tabular,txt,tsv"
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72 label="Tree file (optional)" help="Required for phylogenetic measures
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73 (-t/--tree_fp)" optional="True"/>
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74
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75 <param name="min_rare_depth" type="integer" value="10" label="Lower limit
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76 of rarefaction depths" help="(--min_rare_depth)"/>
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77
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78 <param name="max_rare_depth" type="integer" label="Upper limit
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79 of rarefaction depths" help="By default, median sequence/sample count
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80 is used (-e/--max_rare_depth)" optional="True"/>
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81 </inputs>
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82
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83 <outputs>
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84 <data name="alpha_rarefaction_plots" format="html"
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85 label="${tool.name} on ${on_string}: Alpha rarefaction plots"/>
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86
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87 <data format="txt" name="alpha_diversity">
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88 <discover_datasets pattern="__designation__" ext="txt"
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89 directory="alpha_rarefaction/alpha_div_collated" visible="true" />
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90 </data>
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91 </outputs>
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92
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93 <tests>
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94 <test>
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95 </test>
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96 </tests>
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97
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98 <help><![CDATA[
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99
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100 **What it does**
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101
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102 This script performs alpha rarefaction in several steps:
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103
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104 - Generation of rarefied OTU tables
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105 - Computation of alpha diversity metrics for each rarefied OTU table
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106 - Concatenation of alpha diversity results
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107 - Generation of alpha rarefaction plots
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108
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109 More information about this tool is available on
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110 `QIIME documentation <http://qiime.org/scripts/alpha_rarefaction.html>`_.
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111 ]]>
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112 </help>
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113
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114 <citations>
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115 <expand macro="citations" />
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116 </citations>
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117 </tool>