Mercurial > repos > q2d2 > qiime2__feature_table__merge
diff qiime2__feature_table__merge.xml @ 0:6a753c135e34 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 20:00:50 +0000 |
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children | bbef44c4221b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__feature_table__merge.xml Mon Aug 29 20:00:50 2022 +0000 @@ -0,0 +1,109 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2022, QIIME 2 development team. + +Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) +--> +<!-- +This tool was automatically generated by: + q2galaxy (version: 2022.8.1) +for: + qiime2 (version: 2022.8.1) +--> +<tool name="qiime2 feature-table merge" id="qiime2__feature_table__merge" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Combine multiple tables</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version feature_table</version_command> + <command detect_errors="aggressive">q2galaxy run feature_table merge '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="tables" type="data" format="qza" label="tables: List[FeatureTable[Frequency]¹ | FeatureTable[RelativeFrequency]²]" help="[required] The collection of feature tables to be merged." multiple="true"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[Frequency]"/> + <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> + </options> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="overlap_method" type="select" label="overlap_method: Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum')¹ | Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample')²" help="[default: 'error_on_overlapping_sample'] Method for handling overlapping ids."> + <option value="average">average (Str)</option> + <option value="error_on_overlapping_feature">error_on_overlapping_feature (Str)</option> + <option value="error_on_overlapping_sample" selected="true">error_on_overlapping_sample (Str)</option> + <option value="sum">sum (Str)</option> + </param> + </section> + </inputs> + <outputs> + <data name="merged_table" format="qza" label="${tool.name} on ${on_string}: merged_table.qza" from_work_dir="merged_table.qza"/> + </outputs> + <tests> + <test> + <param name="tables" value="merge.test0.feature-table1.qza,merge.test0.feature-table2.qza" ftype="qza"/> + <output name="merged_table" ftype="qza"/> + </test> + <test> + <param name="tables" value="merge.test1.feature-table1.qza,merge.test1.feature-table2.qza,merge.test1.feature-table3.qza" ftype="qza"/> + <conditional name="__q2galaxy__GUI__conditional__overlap_method__"> + <param name="__q2galaxy__GUI__select__" value="sum"/> + <param name="overlap_method" value="sum"/> + </conditional> + <output name="merged_table" ftype="qza"/> + </test> + </tests> + <help> +QIIME 2: feature-table merge +============================ +Combine multiple tables + + +Outputs: +-------- +:merged_table.qza: The resulting merged feature table. + +| + +Description: +------------ +Combines feature tables using the `overlap_method` provided. + +Examples: +--------- + +basic +***** +Using the ``qiime2 feature-table merge`` tool: + #. For *"tables"*, use ctrl-(or command)-click to select the following inputs: + + #. ``#: feature-table1.qza`` + #. ``#: feature-table2.qza`` + + #. Press the ``Execute`` button. + + +three_tables +************ +Using the ``qiime2 feature-table merge`` tool: + #. For *"tables"*, use ctrl-(or command)-click to select the following inputs: + + #. ``#: feature-table1.qza`` + #. ``#: feature-table2.qza`` + #. ``#: feature-table3.qza`` + + #. Expand the ``additional options`` section + + - Set *"overlap_method"* to ``sum`` + + #. Press the ``Execute`` button. + + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>