Mercurial > repos > q2d2 > qiime2__emperor__procrustes_plot

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author q2d2
date Wed, 30 Oct 2024 19:47:05 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 emperor procrustes-plot" id="qiime2__emperor__procrustes_plot" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Visualize and Interact with a procrustes plot</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version emperor</version_command>
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22 <command detect_errors="exit_code">q2galaxy run emperor procrustes_plot '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="reference_pcoa" type="data" format="qza" label="reference_pcoa: PCoAResults" help="[required] The reference ordination matrix to be plotted.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="PCoAResults"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</validator>
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32 </param>
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33 <param name="other_pcoa" type="data" format="qza" label="other_pcoa: PCoAResults" help="[required] The &quot;other&quot; ordination matrix to be plotted (the one that was fitted to the reference).">
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34 <options options_filter_attribute="metadata.semantic_type">
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35 <filter type="add_value" value="PCoAResults"/>
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36 </options>
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37 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</validator>
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38 </param>
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39 <repeat name="metadata" min="1" help="[required] The sample metadata." title="metadata: Metadata">
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40 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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41 <param name="type" type="select" label="metadata: Metadata">
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42 <option value="tsv" selected="true">Metadata from TSV</option>
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43 <option value="qza">Metadata from Artifact</option>
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44 </param>
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45 <when value="tsv">
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46 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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47 </when>
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48 <when value="qza">
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49 <param name="source" type="data" format="qza" label="Metadata Source"/>
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50 </when>
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51 </conditional>
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52 </repeat>
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53 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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54 <param name="m2_stats" type="data" format="qza" optional="true" label="m2_stats: ProcrustesStatistics" help="[optional] The M^2 value of the procrustes analysis &amp; its associated p value.">
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55 <options options_filter_attribute="metadata.semantic_type">
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56 <filter type="add_value" value="ProcrustesStatistics"/>
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57 </options>
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58 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['ProcrustesStatistics']</validator>
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59 </param>
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60 <repeat name="custom_axes" help="[optional] Numeric sample metadata columns that should be included as axes in the Emperor plot." title="custom_axes: List[Str]">
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61 <param name="element" type="text" label="element: Str" help="[required]">
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62 <sanitizer>
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63 <valid initial="string.printable"/>
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64 </sanitizer>
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65 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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66 </param>
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67 </repeat>
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68 <param name="ignore_missing_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_missing_samples: Bool" help="[default: No] This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: &quot;This sample has no metadata&quot;. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata."/>
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69 </section>
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70 </inputs>
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71 <outputs>
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72 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="reference_pcoa" value="procrustes_plot.test0.bc-pcoa-result.qza" ftype="qza"/>
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77 <param name="other_pcoa" value="procrustes_plot.test0.unw-pcoa-result.qza" ftype="qza"/>
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78 <repeat name="metadata">
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79 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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80 <param name="type" value="tsv"/>
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81 <param name="source" value="procrustes_plot.test0.sample-metadata.tsv" ftype="qiime2.tabular"/>
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82 </conditional>
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83 </repeat>
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84 <output name="visualization" ftype="qzv">
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85 <assert_contents>
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86 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
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87 <has_line_matching expression="type: Visualization"/>
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88 </has_archive_member>
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89 </assert_contents>
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90 </output>
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91 </test>
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92 </tests>
0
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93 <help>
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94 QIIME 2: emperor procrustes-plot
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95 ================================
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96 Visualize and Interact with a procrustes plot
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97
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98
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99 Outputs:
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100 --------
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101 :visualization.qzv: &lt;no description&gt;
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102
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103 |
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104
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105 Description:
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106 ------------
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107 Plot two procrustes-fitted matrices
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108
1
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109 Examples:
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110 ---------
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111
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112 procrustes_plot
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113 ***************
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114 Using the ``qiime2 emperor procrustes-plot`` tool:
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115 #. Set *"reference_pcoa"* to ``#: bc-pcoa-result.qza``
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116 #. Set *"other_pcoa"* to ``#: unw-pcoa-result.qza``
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117 #. For *"metadata"*:
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118
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119 - Perform the following steps.
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120
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121 #. Leave as ``Metadata from TSV``
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122 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
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123
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124
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125 #. Press the ``Execute`` button.
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126
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127 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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128 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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129
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130 .. list-table::
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131 :align: left
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132 :header-rows: 1
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133
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134 * - History Name
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135 - *"Name"* to set (be sure to press ``Save``)
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136 * - ``#: qiime2 emperor procrustes-plot [...] : visualization.qzv``
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137 - ``plot.qzv``
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138
0
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139
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140 |
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141
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142 </help>
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143 <citations>
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144 <citation type="doi">10.1186/2047-217X-2-16</citation>
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145 <citation type="doi">10.1016/j.chom.2016.12.009</citation>
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146 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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147 </citations>
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148 </tool>