Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/collect.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 | d86987601022 |
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6:ce6e81622c6a | 7:7bfe1f843858 |
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1 <tool id="mothur_collect_shared" name="Collect.shared" version="1.19.0" force_history_refresh="True"> | 1 <tool id="mothur_collect_shared" name="Collect.shared" version="1.20.0" force_history_refresh="True"> |
2 <description>Generate collector's curves for calculators on OTUs</description> | 2 <description>Generate collector's curves for calculators on OTUs</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='collect.shared' | 5 --cmd='collect.shared' |
6 --result='^mothur.\S+\.logfile$:'$logfile | 6 --result='^mothur.\S+\.logfile$:'$logfile |
27 <param name="label" type="select" label="label - OTU Label filter" multiple="true"> | 27 <param name="label" type="select" label="label - OTU Label filter" multiple="true"> |
28 <help>To filter: select labels to include</help> | 28 <help>To filter: select labels to include</help> |
29 <options from_dataset="otu"> | 29 <options from_dataset="otu"> |
30 <column name="name" index="0"/> | 30 <column name="name" index="0"/> |
31 <column name="value" index="0"/> | 31 <column name="value" index="0"/> |
32 <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> | |
32 <filter type="unique_value" name="unq_lbl" column="0" /> | 33 <filter type="unique_value" name="unq_lbl" column="0" /> |
33 </options> | 34 </options> |
34 </param> | 35 </param> |
35 <param name="groups" type="select" label="groups - Groups filter (uses all groups if none are selected)" multiple="true"> | 36 <param name="groups" type="select" label="groups - Groups filter (uses all groups if none are selected)" multiple="true"> |
36 <help>To filter: select select at least 2 groups</help> | 37 <help>To filter: select select at least 2 groups</help> |
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="calc" type="select" label="calc - Calculators (Uses defaults if none are selected)" multiple="true"> | 45 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none are selected)" multiple="true"> |
44 <options from_file="mothur_calculators.loc"> | 46 <options from_file="mothur_calculators.loc"> |