annotate 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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
1 <tool id="biom_summarize_table" name="Summarize sample or observation data" version="@VERSION@.1">
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
2 <description>in a BIOM table</description>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
3 <macros>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
5 </macros>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
6 <expand macro="requirements" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
7 <expand macro="version_command" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code">
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
9 <![CDATA[
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
10 biom summarize-table
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
11 --input-fp '$input_fp'
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
12 --output-fp '$output_fp'
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
13 $qualitative
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
14 $observations
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
15 ]]>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
16 </command>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
17 <inputs>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
18 <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="Input BIOM table" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
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" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
20 <param argument="--observations" type="boolean" checked="True" truevalue="--observations" falsevalue="" label="Summarize over observations" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
21 </inputs>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
22 <outputs>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
23 <data format="text" name="output_fp"/>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
24 </outputs>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
25 <tests>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
26 <test>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
27 <param name="input_fp" value="input_abundance_1.biom1" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
28 <param name="qualitative" value="" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
29 <param name="observations" value="" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
30 <output name="output_fp" value="summarize" compare="sim_size"/>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
31 </test>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
32 <test>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
33 <param name="input_fp" value="input_abundance_1.biom1" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
34 <param name="qualitative" value="--qualitative" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
35 <param name="observations" value="--observations" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
36 <output name="output_fp" value="summarize_qualitative_observations" compare="sim_size"/>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
37 </test>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
38 </tests>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
39 <help><![CDATA[
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
40 Provides details on the observation counts per sample, including summary statistics, as well as metadata categories associated with samples and observations.
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
41 ]]></help>
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
42 <expand macro="citations" />
8f4407e9891c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff changeset
43 </tool>