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annotate jackknifed_beta_diversity.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_jackknifed_beta_diversity" name="Perform jackknifed UPGMA
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2 clustering" version="1.9.1">
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3
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4 <description>and building jackknifed 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 jackknifed_beta_diversity.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 <regex match="RuntimeWarning: The result contains negative eigenvalues"
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23 source="both"
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24 level="warning"
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25 description="Presence of negative eigenvalues" />
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26 <regex match="Error"
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27 source="both"
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28 level="error"
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29 description="Error" />
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30 </stdio>
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31
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32 <command>
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33 <![CDATA[
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34 jackknifed_beta_diversity.py
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35 -i $otu_table_fp
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36 -m $mapping_fp
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37 -o jackknifed_beta_diversity
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38 -e $seqs_per_sample
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39
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40 #if $tree_fp
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41 -t $tree_fp
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42 #end if
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43
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44 #if $parameter_fp
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45 -p $parameter_fp
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46 #end if
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47
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48 --master_tree $master_tree
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49
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50 $parallel
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51 -O "\${GALAXY_SLOTS:-4}"
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52 &&
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53
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54 python $__tool_directory__/jackknifed_beta_diversity_through_plots_html_generation.py
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55 --data_directory jackknifed_beta_diversity
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56 --html_file $jackknifed_beta_diversity_report
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57 --html_dir $jackknifed_beta_diversity_report.files_path
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58
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59 ]]>
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60 </command>
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61
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62 <inputs>
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63 <param name="otu_table_fp" type="data" format="tabular,txt,tsv,biom"
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64 label="OTU table" help="(-i/--otu_table_fp)"
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65 multiple="True"/>
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66
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67 <param name="mapping_fp" type="data" format="tabular,txt,tsv"
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68 label="Mapping file" help="(-m/--mapping_fp)"
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69 multiple="True"/>
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70
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71 <param name="seqs_per_sample" type="integer" value="" label="Number of
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72 sequences to include in each jackknifed subset"
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73 help="(-e/--seqs_per_sample)"/>
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74
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75 <param name="tree_fp" type="data" format="txt"
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76 label="Tree file (Optional)" help="It is required for phylogenetic
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77 measures (-t/--tree_fp)"
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78 optional="True"/>
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79
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80 <param name="parameter_fp" type="data" format="txt"
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81 label="Parameter file (Optional)" help="It specifies changes to the
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82 default behavior, e.g. beta diversity metrics (-p/--parameter_fp)"
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83 optional="true"/>
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84
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85 <param name="master_tree" type="select"
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86 label="Method for computing master trees in jackknife analysis"
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87 help="(--master_tree)">
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88 <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option>
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89 <option value="full">Tree generated from input (unsubsambled) otu table</option>
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90 </param>
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91
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92 <param name="parallel" type="boolean" label="Run in parallel where
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93 available?" truevalue="--parallel" falsevalue="" checked="true"
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94 help="(-a, --parallel)" />
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95
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96 </inputs>
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97
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98 <outputs>
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99 <data format="html" name="jackknifed_beta_diversity_report"
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100 label="${tool.name} on ${on_string}: Report"/>
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101 </outputs>
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102
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103 <tests>
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104 <test>
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105 </test>
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106 </tests>
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107
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108 <help><![CDATA[
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109 **What it does**
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110
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111 This tool performs jackknifing (repeatedly resampling a subset of the available data from each sample) to measure robustness of individual UPGMA clusters and clusters in PCoA plots.
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112
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113 More information about this tool is available on
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114 `QIIME documentation <http://qiime.org/scripts/jackknifed_beta_diversity.html>`_.
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115 ]]>
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116 </help>
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117
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118 <citations>
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119 <expand macro="citations" />
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120 </citations>
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121 </tool>