Mercurial > repos > iuc > humann2_unpack_pathways

annotate humann2_unpack_pathways.xml @ 2:7f208f1eb64f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 18fea370966f4b87c8180df4afa0f3b138b75908"
author iuc
date Sat, 25 Jan 2020 18:22:11 -0500
parents d2e4fee96dd1
children 3115a530686e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
1 <tool id="humann2_unpack_pathways" name="Unpack pathway abundances to show genes included" version="@WRAPPER_VERSION@.0">
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
2 <description></description>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
3 <macros>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
4 <import>humann2_macros.xml</import>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
5 </macros>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
7 <expand macro="version"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
9 humann2_unpack_pathways
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
10 --input-genes '$input_genes'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
11 --input-pathways '$input_pathways'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
12 #if $gene_mapping
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
13 --gene-mapping '$gene_mapping'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
14 #end if
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
15 #if $pathway_mapping
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
16 --pathway-mapping '$pathway_mapping'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
17 #end if
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
18 $remove_taxonomy
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
19 --output '$output'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
20 ]]></command>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
21 <inputs>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
22 <param name="input_genes" argument="--input-genes" type="data" format="tsv,tabular" label="Gene family or EC abundance file"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
23 <param name="input_pathways" argument="--input-pathways" type="data" format="tsv,tabular" label="Pathway abundance file"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
24 <param name="gene_mapping" argument="--gene-mapping" type="data" format="tsv,tabular" optional="true" label="Gene family to reaction mapping file"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
25 <param name="pathway_mapping" argument="--pathway-mapping" type="data" format="tsv,tabular" optional="true" label="Reaction to pathway mapping file"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
26 <param name="remove_taxonomy" argument="--remove-taxonomy" type="boolean" truevalue="--remove-taxonomy" falsevalue="" checked="false" label="Remove the taxonomy from the output file?"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
27 </inputs>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
28 <outputs>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
29 <data format="tsv" name="output" label="${tool.name} on ${on_string}" />
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
30 </outputs>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
31 <tests>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
32 <test>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
33 <param name="input_genes" value="demo_genefamilies.tsv"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
34 <param name="input_pathways" value="demo_pathabundance.tsv"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
35 <param name="remove_taxonomy" value=""/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
36 <output name="output" md5="993534d3e8fea242066352a0e4d67c8a"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
37 </test>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
38 <test>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
39 <param name="input_genes" value="demo_genefamilies.tsv"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
40 <param name="input_pathways" value="demo_pathabundance.tsv"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
41 <param name="remove_taxonomy" value="--remove-taxonomy"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
42 <output name="output" md5="b145ce760ce656b9e3ddb00d3ff4cf46"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
43 </test>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
44 </tests>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
45 <help><![CDATA[
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
46 @HELP_HEADER@
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
47
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
48 This utility will unpack the pathways to show the genes for each. It adds another level of stratification to the pathway abundance table by including the gene families (or EC) abundances.
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
49 ]]></help>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
50 <expand macro="citations"/>
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
51 </tool>