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annotate beta_diversity_through_plots.xml @ 0:c1bd0c560018 draft default tip

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author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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1 <tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance
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2 matrices" version="1.9.1">
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3
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4 <description>and generate PCoA plots</description>
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5
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9
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10 <expand macro="requirements" />
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11
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12 <version_command><![CDATA[
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13 beta_diversity_through_plots.py --version
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14 ]]>
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15 </version_command>
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17 <stdio>
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18 <regex match="VisibleDeprecationWarning"
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19 source="both"
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20 level="warning"
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21 description="VisibleDeprecationWarning on numpy for `rank`" />
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22 </stdio>
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23
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24 <command>
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25 <![CDATA[
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26 beta_diversity_through_plots.py
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27 -i $otu_table_fp
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28 -m $mapping_fp
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29 -o beta_diversity_through_plots
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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 #if $parameter_fp
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36 -p $parameter_fp
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37 #end if
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38
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39 $parallel
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40 -O "\${GALAXY_SLOTS:-4}"
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41
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42 #if $seqs_per_sample
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43 -e $seqs_per_sample
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44 #end if
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45
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46 $suppress_emperor_plots
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47
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48 &&
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49
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50 python $__tool_directory__/beta_diversity_through_plots_html_generation.py
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51 --data_directory beta_diversity_through_plots
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52 --html_file $beta_diversity_pcoa
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53 --html_dir $beta_diversity_pcoa.files_path
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54
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55 ]]>
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56 </command>
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57
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58 <inputs>
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59 <param name="otu_table_fp" type="data" format="tabular,txt,tsv,biom"
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60 label="OTU table" help="(-i/--otu_table_fp)"
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61 multiple="True"/>
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62
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63 <param name="mapping_fp" type="data" format="tabular,txt,tsv"
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64 label="Mapping file" help="(-m/--mapping_fp)"
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65 multiple="True"/>
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66
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67 <param name="tree_fp" type="data" format="txt"
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68 label="Tree file (Optional)" help="(-t/--tree_fp)"
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69 optional="True"/>
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70
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71 <param name="parameter_fp" type="data" format="txt"
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72 label="Parameter file (Optional)" help="It specifies changes to the default
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73 behavior, e.g. beta diversity metrics (-p/--parameter_fp)"
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74 optional="true"/>
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75
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76 <param name="color_by_all_fields" type="text" label="Colored mapping
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77 fields" optional="True" help="Can be included only fields with
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78 greater than one value and fewer values than the number of samples
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79 (--color_by_all_fields)" />
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80
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81 <param name="parallel" type="boolean" label="Run in parallel where
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82 available?" truevalue="--parallel" falsevalue="" checked="False"
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83 help="(-a, --parallel)" />
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84
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85 <param name="seqs_per_sample" type="integer" label="Depth of coverage for
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86 even sampling (Optional)" help="(-e/--seqs_per_sample)" optional="True"/>
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87
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88 <param name="suppress_emperor_plots" type="boolean" label="Generate
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89 emperor plots?" truevalue="" falsevalue="--suppress_emperor_plots" checked="True"
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90 help="(--suppress_emperor_plots)" />
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91
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92 </inputs>
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93
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94 <outputs>
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95 <data format="txt" name="beta_diversity_matrix">
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96 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dm\.txt" ext="txt"
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97 directory="beta_diversity_through_plots" visible="true" />
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98 </data>
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99
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100 <data format="txt" name="beta_diversity_pc">
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101 <discover_datasets pattern="(?P&lt;designation&gt;.+)_pc\.txt" ext="txt"
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102 directory="beta_diversity_through_plots" visible="true" />
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103 </data>
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104
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105 <data format="html" name="beta_diversity_pcoa"
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106 label="${tool.name} on ${on_string}: PCoA"/>
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107 </outputs>
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108
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109 <tests>
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110 <test>
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111 </test>
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112 </tests>
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113
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114 <help><![CDATA[
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115 **What it does**
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116
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117 This tool computes beta diversity distance matrices and generates PCoA plots in
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118 several steps
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119
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120 - Performs beta diversity analysis
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121 - Performs principal coordinate analysis
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122 - Generates 3D PCoA Plots
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123
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124 More information about this tool is available on
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125 `QIIME documentation <http://qiime.org/scripts/beta_diversity_through_plots.html>`_.
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126 ]]>
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127 </help>
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128
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129 <citations>
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130 <expand macro="citations" />
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131 </citations>
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132 </tool>