Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/normalize.shared.xml @ 7:7bfe1f843858
Support Mothur v1.20
trim.seqs - added name parameter and optional trim.names output
phylo.diversity - group optional, put group and groups in conditional - breaks
get.lineage remove.lineage - allow multiple taxons
dist.shared - added processors
consensus.seqs - add cutoff parameter
trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs
new tools - chimera.uchime deunique.tree count.seqs
shared/relabund files - Column headings
refactor lib/galaxy/datatypes/metagenomics.py
add filters to label and group selects in tool configs
mothur_wrapper.py updated with new tools params
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 27 Jun 2011 10:12:25 -0500 |
parents | e990ac8a0f58 |
children | bfbaf823be4c |
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6:ce6e81622c6a | 7:7bfe1f843858 |
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1 <tool id="mothur_normalize_shared" name="Normalize.shared" version="1.19.0"> | 1 <tool id="mothur_normalize_shared" name="Normalize.shared" version="1.20.0"> |
2 <description>Normalize the number of sequences per group to a specified level</description> | 2 <description>Normalize the number of sequences per group to a specified level</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='normalize.shared' | 5 --cmd='normalize.shared' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.norm\.shared$:'$shared | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.norm\.shared$:'$shared |
28 <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> | 28 <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> |
29 <param name="label" type="select" label="label - OTU Labels" multiple="true"> | 29 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
30 <options from_dataset="otu"> | 30 <options from_dataset="otu"> |
31 <column name="name" index="0"/> | 31 <column name="name" index="0"/> |
32 <column name="value" index="0"/> | 32 <column name="value" index="0"/> |
33 <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> | |
33 <filter type="unique_value" name="unq_lbl" column="0" /> | 34 <filter type="unique_value" name="unq_lbl" column="0" /> |
34 </options> | 35 </options> |
35 </param> | 36 </param> |
36 <param name="groups" type="select" label="groups - Groups to include" multiple="true"> | 37 <param name="groups" type="select" label="groups - Groups to include" multiple="true"> |
37 <options from_dataset="otu"> | 38 <options from_dataset="otu"> |
38 <column name="name" index="1"/> | 39 <column name="name" index="1"/> |
39 <column name="value" index="1"/> | 40 <column name="value" index="1"/> |
41 <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> | |
40 <filter type="unique_value" name="unq_grp" column="1" /> | 42 <filter type="unique_value" name="unq_grp" column="1" /> |
41 </options> | 43 </options> |
42 </param> | 44 </param> |
43 <param name="norm" type="integer" value="0" label="norm - Number to normalize to (Uses default if < 1)" | 45 <param name="norm" type="integer" value="0" label="norm - Number to normalize to (Uses default if < 1)" |
44 help="By default this is set to the number of sequences in your smallest group."/> | 46 help="By default this is set to the number of sequences in your smallest group."/> |