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comparison mothur/tools/mothur/phylo.diversity.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_phylo_diversity" name="Phylo.diversity" version="1.19.0"> 1 <tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.20.0">
2 <description>Alpha Diversity calculates unique branch length</description> 2 <description>Alpha Diversity calculates unique branch length</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='phylo.diversity' 5 --cmd='phylo.diversity'
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.phylodiv\.summary$:'$summary_out,'^\S+\.phylodiv$:'$collectors_out,'^\S+\.rarefaction$:'$rarefaction_out 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.phylodiv\.summary$:'$summary_out,'^\S+\.phylodiv$:'$collectors_out,'^\S+\.rarefaction$:'$rarefaction_out
7 --outputdir='$logfile.extra_files_path' 7 --outputdir='$logfile.extra_files_path'
8 --tree=$tree 8 --tree=$tree
9 #if $group.__str__ != "None" and len($group.__str__) > 0: 9 #if $grouping.use:
10 --group='$group' 10 #if $grouping.group.__str__ != "None" and len($grouping.group.__str__) > 0:
11 #end if 11 --group='$grouping.group'
12 #if $groups.__str__ != "None" and len($groups.__str__) > 0: 12 #end if
13 --groups='$groups' 13 #if $grouping.groups.__str__ != "None" and len($grouping.groups.__str__) > 0:
14 --groups='$grouping.groups'
15 #end if
14 #end if 16 #end if
15 #if $name.__str__ != "None" and len($name.__str__) > 0: 17 #if $name.__str__ != "None" and len($name.__str__) > 0:
16 --name='$name' 18 --name='$name'
17 #end if 19 #end if
18 #if int($iters.__str__) > 0: 20 #if int($iters.__str__) > 0:
30 --processors=2 32 --processors=2
31 </command> 33 </command>
32 <inputs> 34 <inputs>
33 <!-- list,group or shared --> 35 <!-- list,group or shared -->
34 <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/> 36 <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/>
35 <param name="group" type="data" format="groups" label="group - Group file for the tree"/> 37 <conditional name="grouping">
36 <param name="groups" type="select" label="groups - Groups to display" multiple="true"> 38 <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Analyze by group using a Group file"/>
37 <options from_dataset="group"> 39 <when value="yes">
38 <column name="name" index="1"/> 40 <param name="group" type="data" format="groups" label="group - Group file for the tree"/>
39 <column name="value" index="1"/> 41 <param name="groups" type="select" label="groups - Groups to display" multiple="true">
40 <filter type="unique_value" name="unq_grp" column="1" /> 42 <help>All groups displayed if none are selected.</help>
41 </options> 43 <options from_dataset="group">
42 </param> 44 <column name="name" index="1"/>
45 <column name="value" index="1"/>
46 <filter type="unique_value" name="unq_grp" column="1" />
47 </options>
48 </param>
49 </when>
50 <when value="no"/>
51 </conditional> <!-- use_groups -->
43 <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file for the tree"/> 52 <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file for the tree"/>
44 <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/> 53 <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/>
45 <param name="freq" type="float" value="0.0" label="freq - Reporting frequency" 54 <param name="freq" type="float" value="0.0" label="freq - Reporting frequency"
46 help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/> 55 help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/>
47 56