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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 950bc3657a7bd6975337324bd0f1d0e5c0afc0f4
author iuc
date Fri, 15 Mar 2024 15:25:33 +0000
parents aab88b1cea31
children
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9d84e99a4253 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4ca0a67fd4126f8b2a135b6cb7894042e980b39a"
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1 <tool id="biom_subset_table" name="Subset" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>a BIOM table</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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aab88b1cea31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 2230d399cc6a526674f192099f00632dcc931e8c
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code">
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10 <![CDATA[
806ff6f90364 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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11 biom subset-table
806ff6f90364 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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12 --input-json-fp '$input_json_fp'
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13 --output-fp '$output_fp'
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14 --axis '$axis'
806ff6f90364 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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15 --ids '$ids'
806ff6f90364 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param argument="--input-json-fp" type="data" format="biom1" label="BIOM table to subset" />
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20 <param argument="--axis" type="select" label="The axis to subset over">
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21 <option value="sample" selected="True">Sample</option>
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22 <option value="observation">Observation</option>
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23 </param>
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24 <param argument="--ids" type="data" format="txt,tabular" label="file containing a single column of IDs to retain" />
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25 </inputs>
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26 <outputs>
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27 <data format="biom1" name="output_fp"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input_json_fp" value="input_abundance_1.biom1" />
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32 <param name="axis" value="sample" />
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33 <param name="ids" value="sample_subsetting" />
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34 <output name="output_fp" file="subset_samples.biom" ftype="biom1" compare="sim_size"/>
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35 </test>
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36 <test>
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37 <param name="input_json_fp" value="input_abundance_1.biom1" />
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38 <param name="axis" value="observation" />
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39 <param name="ids" value="observation_subsetting" />
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40 <output name="output_fp" file="subset_observations.biom" ftype="biom1" compare="sim_size"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 Subset a BIOM table, over either observations or samples, without fully parsing it. This command is intended to assist in working with very large tables when tight on memory, or as a lightweight way to subset a full table. Currently, it is possible to produce tables with rows or columns (observations or samples) that are fully zeroed.
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45 ]]></help>
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46 <expand macro="citations" />
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47 </tool>