Mercurial > repos > iuc > humann2_strain_profiler

annotate humann2_strain_profiler.xml @ 3:1a089e6ba8a6 draft default tip

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 8d953926efdf23d8c3fb8719341dff51a55a92f2"
author iuc
date Sun, 28 Mar 2021 06:47:33 +0000
parents 25d77fa8a6a6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
25d77fa8a6a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
iuc
parents: 0
diff changeset
1 <tool id="humann2_strain_profiler" name="Make strain profiles" version="@WRAPPER_VERSION@.1">
0
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
2 <description></description>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
3 <macros>
10eda79d5af4 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>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
5 </macros>
2
25d77fa8a6a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
iuc
parents: 0
diff changeset
6 <expand macro="stdio"/>
0
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
8 <expand macro="version"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
10 humann2_strain_profiler
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
11 --input '$input'
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
12 --critical_mean '$critical_mean'
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
13 --critical_count '$critical_count'
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
14 --pinterval '$pinterval_1' '$pinterval_2'
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
15 --critical_samples '$critical_samples'
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
16 #if str($limit) != ''
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
17 --limit '$limit'
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
18 #end if
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
19 ]]></command>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
20 <inputs>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
21 <param argument="--input" type="data" format="tsv,tabular,biom1" label="Merged gene families output for two or more samples"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
22 <param argument="--critical_mean" type="float" value="10.0" label="Default mean non-zero gene abundance for inclusion"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
23 <param argument="--critical_count" type="integer" value="500" label="Default non-zero number of genes for inclusion"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
24 <param name="pinterval_1" type="float" value="1e-10" label="Low prevalence threshold" help="Only genes with prevalence higher than the threshold are allowed"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
25 <param name="pinterval_2" type="float" value="1" label="High prevalence threshold" help="Only genes with prevalence lower than the threshold are allowed"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
26 <param argument="--critical_samples" type="integer" value="2" label="Threshold number of samples having strain"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
27 <param argument="--limit" type="text" value="" optional="true" label="Limit output to species matching a particular pattern?" help="e.g. 'Streptococcus'"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
28 </inputs>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
29 <outputs>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
30 <collection name="output" type="list" label="${tool.name} on ${on_string}">
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
31 <discover_datasets pattern="(?P&lt;designation&gt;.+)-strain_profile.tsv" format="tsv" directory="."/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
32 </collection>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
33 </outputs>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
34 <tests>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
35 <test>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
36 <param name="input" value="strain_profiler-input.txt"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
37 <param name="critical_mean" value="1"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
38 <param name="critical_count" value="2"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
39 <param name="pinterval_1" value="1e-10"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
40 <param name="pinterval_2" value="1"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
41 <param name="critical_samples" value="2"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
42 <output_collection name="output" type="list">
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
43 <element name="s1" md5="09b0645f058ecdaccb3af12f655198a0"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
44 <element name="s2" md5="935698addd30312500b3cb1139c7d24b"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
45 </output_collection>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
46 </test>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
47 </tests>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
48 <help><![CDATA[
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
49 @HELP_HEADER@
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
50
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
51 This script is currently at an experimental stage. Please use with caution.
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
52
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
53 The HUMAnN2 script humann2_strain_profiler can help explore strain-level variation in your data. This approach assumes you have run HUMAnN2 on a series of samples and then merged the resulting genefamilies.tsv tables with humann2_merge_tables. Cases will arise in which the same species was detected in two or more samples, but gene families within that species were not consistently present across samples. For example, four samples may contain the species Dialister invisus, but only two samples contain the gene family UniRef50_Q5WII6 within Dialister invisus. This is a form of strain-level variation in the Dialister invisus species: one which we can connect directly to function based on annotations of the UniRef50_Q5WII6 gene family.
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
54
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
55 humann2_strain_profiler first looks for (species, sample) pairs where (i) a large number of gene families within the species were identified (default: 500) and (ii) the mean abundance of detected genes was high (default: mean > 10 RPK). For species that meet these criteria, we can infer that absent gene families are likely to be truly absent, as opposed to undersampled. Simulations suggest that the cutoff of 10 RPK results in a false negative rate below 0.001 (i.e. for every 1000 genes identified as absent, at most one would be present but missed due to undersampling). For a given species, if at least two samples pass these criteria, the species and passing samples are sliced from the merged table and saved as a strain profile.
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
56
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
57 Strain profiles can be additionally restricted to a subset of species (e.g. those from a particular genus) or to gene families with a high level of variability in the population (e.g. present in fewer than 80% of samples but more than 20% of samples). Additional thresholds (e.g. the minimum non-zero mean) can be configured with command line parameters.
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
58 ]]></help>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
59 <expand macro="citations"/>
10eda79d5af4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
60 </tool>