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annotate core_diversity_analyses.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_core_diversity" name="Compute core set of diversity analyses" version="1.9.1">
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2 <description></description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements" />
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9
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10 <version_command><![CDATA[
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11 core_diversity_analyses.py --version
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12 ]]>
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13 </version_command>
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14
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15 <command>
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16 <![CDATA[
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17 core_diversity_analyses.py
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18 -i $input_biom_fp
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19 -o core_diversity_analyses
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20 -m $mapping_fp
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21 -e $sampling_depth
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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 $parallel
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28 -O "\${GALAXY_SLOTS:-4}"
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29
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30 #if $phylogenetic.nonphylogenetic_diversity
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31 --nonphylogenetic_diversity
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32 #else
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33 -t $phylogenetic.tree_fp
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34 #end if
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35
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36 $suppress_taxa_summary
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37 $suppress_beta_diversity
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38 $suppress_alpha_diversity
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39 $suppress_group_significance
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40
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41 #if $categories
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42 -c $categories
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43 #end if
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44
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45 &&
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46 mkdir -p $html_report.files_path
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47 &&
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48 cp -r core_diversity_analyses/* $html_report.files_path
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49 &&
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50 mv $html_report.files_path/index.html $html_report
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51 ]]>
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52 </command>
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53
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54 <inputs>
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55 <param name="input_biom_fp" type="data" format="tabular,txt,tsv,biom"
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56 label="OTU table" help="(-i/--input_biom_fp)"/>
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57
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58 <param name="mapping_fp" type="data" format="tabular,txt,tsv"
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59 label="Mapping file" help="(-m/--mapping_fp)"/>
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60
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61 <param name="sampling_depth" type="integer" value="" label="Sequencing
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62 depth to use for even sub-sampling and maximum rarefaction depth"
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63 help="To decide this value, review the output of the
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64 ‘biom summarize-table’ (-e/--sampling_depth)"/>
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65
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66 <param name="parameter_fp" type="data" format="txt"
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67 label="Parameter file" help="It specifies changes to the default
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68 behavior (-p/--parameter_fp)" optional="true"/>
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69
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70 <param name="parallel" type="boolean" label="Run in parallel where
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71 available?" truevalue="--parallel" falsevalue="" checked="true"
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72 help="(-a, --parallel)" />
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73
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74 <conditional name="phylogenetic">
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75 <param name="nonphylogenetic_diversity" type="boolean" label="Apply
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76 non-phylogenetic alpha (chao1 and observed_otus) and beta (bray_curtis)
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77 diversity calculations?" truevalue="--nonphylogenetic_diversity"
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78 falsevalue="" checked="false" help="This is useful if, for example,
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79 when working with non-amplicon BIOM tables, or if a reliable tree
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80 is not available (--nonphylogenetic_diversity)" />
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81 <when value="false" >
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82 <param name="tree_fp" type="data" format="txt"
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83 label="Tree file" help="(-t/--tree_fp)"/>
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84 </when>
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85 <when value="true" />
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86 </conditional>
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87
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88 <param name="suppress_taxa_summary" type="boolean" label="Suppress
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89 generation of taxa summary plots?" truevalue="--suppress_taxa_summary"
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90 falsevalue="" checked="False" help="(--suppress_taxa_summary)" />
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91
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92 <param name="suppress_beta_diversity" type="boolean" label="Suppress
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93 beta diversity analyses?" truevalue="--suppress_beta_diversity"
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94 falsevalue="" checked="False" help="(--suppress_beta_diversity)" />
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95
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96 <param name="suppress_alpha_diversity" type="boolean" label="Suppress
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97 alpha diversity analyses?" truevalue="--suppress_alpha_diversity"
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98 falsevalue="" checked="False" help="(--suppress_alpha_diversity)" />
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99
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100 <param name="suppress_group_significance" type="boolean" label="Suppress
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101 OTU/category significance analysis?" truevalue="--suppress_group_significance"
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102 falsevalue="" checked="False" help="(--suppress_group_significance)" />
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103
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104 <param name="categories" type="text" value="" label="Metadata category or
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105 categories to compare for categorical analyses (optional)"
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106 help="The column headers in the mapping file should be passed as a
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107 comma-separated list. By default, no categorical analyses are performed
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108 (-c/--categories)" optional="true"/>
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109
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110 </inputs>
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111
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112 <outputs>
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113 <data name="html_report" format="html"
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114 label="${tool.name} on ${on_string}: Core diversity report" />
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115 </outputs>
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116
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117 <tests>
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118 <test>
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119 </test>
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120 </tests>
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121
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122 <help><![CDATA[
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123
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124 **What it does?**
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125
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126 This tool calculates alpha diversity, or within-sample diversity, using an
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127 OTU table.
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128
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129 The resulting file(s) is a tab-delimited text file, where the columns correspond
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130 to alpha diversity metrics and the rows correspond to samples and their calculated
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131 diversity measurements. When a folder is given as input (-i), the script processes
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132 every otu table file in the given folder, and creates a corresponding file in the
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133 output directory.
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134
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135 More information about this tool is available on
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136 `QIIME documentation <http://qiime.org/scripts/alpha_diversity.html>`_.
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137 ]]>
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138 </help>
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139
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140 <citations>
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141 <expand macro="citations" />
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142 </citations>
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143 </tool>