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comparison biom_subset_table.xml @ 0:245950fb3a66 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
author iuc
date Wed, 31 May 2017 11:19:11 -0400
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children 9f3f3ae3e82c
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1 <tool id="biom_subset_table" name="Subset" version="@VERSION@.1">
2 <description>a BIOM table</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
8 <command detect_errors="exit_code">
9 <![CDATA[
10 biom subset-table
11 --input-json-fp '$input_json_fp'
12 --output-fp '$output_fp'
13 --axis '$axis'
14 --ids '$ids'
15 ]]>
16 </command>
17 <inputs>
18 <param name="input_json_fp" argument="--input-json-fp" type="data" format="biom1" label="BIOM table to subset" />
19 <param argument="--axis" type="select" label="The axis to subset over">
20 <option value="sample" selected="True">Sample</option>
21 <option value="observation">Observation</option>
22 </param>
23 <param argument="--ids" type="data" format="text,tabular" label="file containing a single column of IDs to retain" />
24 </inputs>
25 <outputs>
26 <data format="biom1" name="output_fp"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="input_json_fp" value="input_abundance_1.biom1" />
31 <param name="axis" value="sample" />
32 <param name="ids" value="sample_subsetting" />
33 <output name="output_fp" file="subset_samples.biom" ftype="biom1" compare="sim_size"/>
34 </test>
35 <test>
36 <param name="input_json_fp" value="input_abundance_1.biom1" />
37 <param name="axis" value="observation" />
38 <param name="ids" value="observation_subsetting" />
39 <output name="output_fp" file="subset_observations.biom" ftype="biom1" compare="sim_size"/>
40 </test>
41 </tests>
42 <help><![CDATA[
43 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.
44 ]]></help>
45 <expand macro="citations" />
46 </tool>