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comparison mothur/tools/mothur/dist.shared.xml @ 7:7bfe1f843858

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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>
date Mon, 27 Jun 2011 10:12:25 -0500
parents e990ac8a0f58
children 4f797d3eee3a
comparison
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6:ce6e81622c6a 7:7bfe1f843858
1 <tool id="mothur_dist_shared" name="Dist.shared" version="1.19.0" force_history_refresh="True"> 1 <tool id="mothur_dist_shared" name="Dist.shared" version="1.20.0" force_history_refresh="True">
2 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description> 2 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='dist.shared' 5 --cmd='dist.shared'
6 --result='^mothur.\S+\.logfile$:'$logfile 6 --result='^mothur.\S+\.logfile$:'$logfile
28 --calc=$calc 28 --calc=$calc
29 #end if 29 #end if
30 #if $output.__str__ != "None" and len($output.__str__) > 0: 30 #if $output.__str__ != "None" and len($output.__str__) > 0:
31 --output=$output 31 --output=$output
32 #end if 32 #end if
33 --processors=2
33 </command> 34 </command>
34 <inputs> 35 <inputs>
35 <!-- list,group or shared --> 36 <!-- list,group or shared -->
36 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> 37 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
37 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true"> 38 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true">
38 <options from_dataset="otu"> 39 <options from_dataset="otu">
39 <column name="name" index="0"/> 40 <column name="name" index="0"/>
40 <column name="value" index="0"/> 41 <column name="value" index="0"/>
42 <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/>
41 <filter type="unique_value" name="unq_lbl" column="0" /> 43 <filter type="unique_value" name="unq_lbl" column="0" />
42 </options> 44 </options>
43 </param> 45 </param>
44 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"> 46 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
45 <options from_dataset="otu"> 47 <options from_dataset="otu">
46 <column name="name" index="1"/> 48 <column name="name" index="1"/>
47 <column name="value" index="1"/> 49 <column name="value" index="1"/>
50 <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/>
48 <filter type="unique_value" name="unq_grp" column="1" /> 51 <filter type="unique_value" name="unq_grp" column="1" />
49 </options> 52 </options>
50 </param> 53 </param>
51 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> 54 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
52 <options from_file="mothur_calculators.loc"> 55 <options from_file="mothur_calculators.loc">