annotate humann_genefamilies_genus_level @ 5:e88b731dad59 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit ccaedf215676efa9afe412f2f8c95d8220c885ee
author iuc
date Sun, 13 Aug 2023 17:00:09 +0000
parents 26ce946f4da9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
1 <!-- The tool is broken with current version of HUMAnN. Once it will be fixed (PR merged), we can update this wrapper and add the XML extension to enable it -->
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
2 <tool id="humann_genefamilies_genus_level" name="Create a genus level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
3 <description>gene families and pathways from HUMAnN species level gene families</description>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
4 <macros>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
5 <import>macros.xml</import>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
6 </macros>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
7 <expand macro="edam_ontology"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
8 <expand macro="requirements"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
9 <expand macro="version"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
11 humann_genefamilies_genus_level
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
12 --input '$input'
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
13 --output '$gene_families'
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
14 &&
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
15 humann
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
16 --input '$gene_families'
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
17 --output '$pathways'
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
18 ]]></command>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
19 <inputs>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
20 <param argument="--input" type="data" format="tsv,tabular" label="Species level gene families" help="Direct output from HUMAnN"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
21 </inputs>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
22 <outputs>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
23 <data name="gene_families" format="tabular" label="${tool.name} on ${on_string}: Genus level gene families"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
24 <data name="pathways" format="tabular" label="${tool.name} on ${on_string}: Genus level pathways"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
25 </outputs>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
26 <tests>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
27 <test expect_num_outputs="1">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
28 <param name="input" value="demo_genefamilies.tsv"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
29 <output name="gene_families" ftype="tabular" value="genus-level-gene-families.tsv" compare="sim_size">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
30 <assert_contents>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
31 <has_text text="humann_Abundance"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
32 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
33 <has_n_columns n="2"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
34 </assert_contents>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
35 </output>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
36 <output name="pathways" ftype="tabular" value="genus-level-pathways.tsv" compare="sim_size">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
37 <assert_contents>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
38 <has_text text="humann_Abundance"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
39 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
40 <has_n_columns n="2"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
41 </assert_contents>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
42 </output>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
43 </test>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
44 </tests>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
45 <help><![CDATA[
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
46 @HELP_HEADER@
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
47
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
48 By default, the gene families and pathways output files from HUMAnN are species level.
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
49 This tool generates genus level gene families and pathways
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
50 ]]></help>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
51 <expand macro="citations"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
parents:
diff changeset
52 </tool>