Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/cluster.split.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 4f797d3eee3a |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_cluster_split" name="Cluster.split" version="1.16.0"> | 1 <tool id="mothur_cluster_split" name="Cluster.split" version="1.19.0"> |
2 <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description> | 2 <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='cluster.split' | 5 --cmd='cluster.split' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist,'^\S+\.dist$:'$dist_out |
7 --outputdir='$logfile.extra_files_path' | 7 --outputdir='$logfile.extra_files_path' |
8 #if $splitby.splitmethod == "distance": | 8 #if $splitby.splitmethod == "distance": |
9 #if $splitby.matrix.format == "column": | 9 #if $splitby.matrix.format == "column": |
10 --column=$splitby.matrix.dist | 10 --column=$splitby.matrix.dist |
11 --name=$splitby.matrix.name | 11 --name=$splitby.matrix.name |
70 </conditional> | 70 </conditional> |
71 </when> | 71 </when> |
72 <when value="classify"> | 72 <when value="classify"> |
73 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> | 73 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> |
74 <param name="name" type="data" format="names" label="name - Sequences Name reference"/> | 74 <param name="name" type="data" format="names" label="name - Sequences Name reference"/> |
75 <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/> | 75 <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/> |
76 <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" | 76 <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" |
77 help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/> | 77 help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/> |
78 </when> | 78 </when> |
79 <when value="fasta"> | 79 <when value="fasta"> |
80 <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/> | 80 <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/> |
81 <param name="name" type="data" format="names" label="name - Sequences Name reference"/> | 81 <param name="name" type="data" format="names" label="name - Sequences Name reference"/> |
82 <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/> | 82 <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/> |
83 <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" | 83 <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" |
84 help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/> | 84 help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/> |
85 </when> | 85 </when> |
86 </conditional> <!-- splitby --> | 86 </conditional> <!-- splitby --> |
87 <param name="method" type="select" label="method - Select a Clustering Method" help=""> | 87 <param name="method" type="select" label="method - Select a Clustering Method" help=""> |
88 <option value="furthest" selected="true">Furthest neighbor</option> | 88 <option value="furthest">Furthest neighbor</option> |
89 <option value="nearest">Nearest neighbor</option> | 89 <option value="nearest">Nearest neighbor</option> |
90 <option value="average">Average neighbor</option> | 90 <option value="average" selected="true">Average neighbor</option> |
91 </param> | 91 </param> |
92 <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" | 92 <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" |
93 help="Ignore pairwise distances larger than this, a common value would be 0.10"/> | 93 help="Ignore pairwise distances larger than this, a common value would be 0.10"/> |
94 <param name="hard" type="boolean" checked="false" truevalue="--hard=true" falsevalue="" label="hard - Use hard cutoff instead of rounding" | 94 <param name="hard" type="boolean" checked="true" truevalue="--hard=true" falsevalue="--hard=true" label="hard - Use hard cutoff instead of rounding" |
95 help=""/> | 95 help=""/> |
96 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" | 96 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" |
97 help="Set higher precision for longer genome scale sequence lengths"> | 97 help="Set higher precision for longer genome scale sequence lengths"> |
98 <option value="10">.1</option> | 98 <option value="10">.1</option> |
99 <option value="100" selected="true">.01</option> | 99 <option value="100" selected="true">.01</option> |
108 <outputs> | 108 <outputs> |
109 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 109 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
110 <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> | 110 <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> |
111 <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> | 111 <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> |
112 <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> | 112 <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> |
113 <data format="pair.dist" name="dist_out" label="${tool.name} on ${on_string}: Column dist"> | |
114 <filter>splitby.splitmethod == 'fasta' </filter> | |
115 </data> | |
113 </outputs> | 116 </outputs> |
114 <requirements> | 117 <requirements> |
115 <requirement type="binary">mothur</requirement> | 118 <requirement type="binary">mothur</requirement> |
116 </requirements> | 119 </requirements> |
117 <tests> | 120 <tests> |