comparison biom_summarize_table.xml @ 0:8f4407e9891c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
author iuc
date Wed, 11 Sep 2019 12:39:57 -0400
parents
children 2cc55cbcb4a3
comparison
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-1:000000000000 0:8f4407e9891c
1 <tool id="biom_summarize_table" name="Summarize sample or observation data" version="@VERSION@.1">
2 <description>in 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 summarize-table
11 --input-fp '$input_fp'
12 --output-fp '$output_fp'
13 $qualitative
14 $observations
15 ]]>
16 </command>
17 <inputs>
18 <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="Input BIOM table" />
19 <param argument="--qualitative" type="boolean" checked="True" truevalue="--qualitative" falsevalue="" label="Present counts as number of unique observation ids per sample, rather than counts of observations per sample" />
20 <param argument="--observations" type="boolean" checked="True" truevalue="--observations" falsevalue="" label="Summarize over observations" />
21 </inputs>
22 <outputs>
23 <data format="text" name="output_fp"/>
24 </outputs>
25 <tests>
26 <test>
27 <param name="input_fp" value="input_abundance_1.biom1" />
28 <param name="qualitative" value="" />
29 <param name="observations" value="" />
30 <output name="output_fp" value="summarize" compare="sim_size"/>
31 </test>
32 <test>
33 <param name="input_fp" value="input_abundance_1.biom1" />
34 <param name="qualitative" value="--qualitative" />
35 <param name="observations" value="--observations" />
36 <output name="output_fp" value="summarize_qualitative_observations" compare="sim_size"/>
37 </test>
38 </tests>
39 <help><![CDATA[
40 Provides details on the observation counts per sample, including summary statistics, as well as metadata categories associated with samples and observations.
41 ]]></help>
42 <expand macro="citations" />
43 </tool>