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comparison mothur/tools/mothur/phylo.diversity.xml @ 2:e990ac8a0f58

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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:39:06 -0400
parents fcc0778f6987
children 7bfe1f843858
comparison
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1:fcc0778f6987 2:e990ac8a0f58
1 <tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.16.0"> 1 <tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.19.0">
2 <description>Alpha Diversity calculate 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 --READ_cmd='read.tree' 8 --tree=$tree
9 --READ_tree=$tree
10 #if $group.__str__ != "None" and len($group.__str__) > 0: 9 #if $group.__str__ != "None" and len($group.__str__) > 0:
11 --READ_group='$group' 10 --group='$group'
12 #end if 11 #end if
13 #if $groups.__str__ != "None" and len($groups.__str__) > 0: 12 #if $groups.__str__ != "None" and len($groups.__str__) > 0:
14 --groups='$groups' 13 --groups='$groups'
14 #end if
15 #if $name.__str__ != "None" and len($name.__str__) > 0:
16 --name='$name'
15 #end if 17 #end if
16 #if int($iters.__str__) > 0: 18 #if int($iters.__str__) > 0:
17 --iters=$iters 19 --iters=$iters
18 #end if 20 #end if
19 #if float($freq.__str__) > 0: 21 #if float($freq.__str__) > 0:
20 --freq=$freq 22 --freq=$freq
21 #end if 23 #end if
22 $scale 24 $scale
23 $summary
24 $collect 25 $collect
25 $rarefy 26 $rarefy
27 #if len($rarefy.__str__) > 0 or len($collect.__str__) > 0:
28 $summary
29 #end if
26 --processors=2 30 --processors=2
27 </command> 31 </command>
28 <inputs> 32 <inputs>
29 <!-- list,group or shared --> 33 <!-- list,group or shared -->
30 <param name="tree" type="data" format="tre" label="read.tree(tree=) - Phylogenetic Tree"/> 34 <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/>
31 <param name="group" type="data" format="groups" label="read.tree(group=) - Group file for the tree"/> 35 <param name="group" type="data" format="groups" label="group - Group file for the tree"/>
32 <param name="groups" type="select" label="groups - Groups to display" multiple="true"> 36 <param name="groups" type="select" label="groups - Groups to display" multiple="true">
33 <options from_dataset="group"> 37 <options from_dataset="group">
34 <column name="name" index="1"/> 38 <column name="name" index="1"/>
35 <column name="value" index="1"/> 39 <column name="value" index="1"/>
36 <filter type="unique_value" name="unq_grp" column="1" /> 40 <filter type="unique_value" name="unq_grp" column="1" />
37 </options> 41 </options>
38 </param> 42 </param>
43 <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file for the tree"/>
39 <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/> 44 <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/>
40 <param name="freq" type="float" value="0.0" label="freq - Reporting frequency" 45 <param name="freq" type="float" value="0.0" label="freq - Reporting frequency"
41 help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/> 46 help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/>
42 47
43 <param name="scale" type="boolean" truevalue="--scale=true" falsevalue="" checked="false" label="scale - Scale output to the number of sequences sampled" /> 48 <param name="scale" type="boolean" truevalue="--scale=true" falsevalue="" checked="false" label="scale - Scale output to the number of sequences sampled" />