Mercurial > repos > iuc > mothur_pre_cluster

annotate pre.cluster.xml @ 1:e277ab688993 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:09:17 -0400
parents 4b5b8a603f52
children d6bed1e2df21
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
1 <tool profile="16.07" id="mothur_pre_cluster" name="Pre.cluster" version="@WRAPPER_VERSION@.0">
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
2 <description>Remove sequences due to pyrosequencing errors</description>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
3 <macros>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
4 <import>macros.xml</import>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
5 </macros>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
1
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
7 <expand macro="stdio"/>
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
8 <expand macro="version_command"/>
1
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
9 <command><![CDATA[
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
10 @SHELL_OPTIONS@
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
11
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
12 ## create symlinks to input datasets
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
13 ln -s "$fasta" fasta.dat &&
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
14 ln -s "$name" name.dat &&
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
15 ln -s "$group" group.dat &&
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
16
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
17 echo 'pre.cluster(
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
18 fasta=fasta.dat,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
19 #if $name.is_of_type("mothur.names"):
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
20 name=name.dat,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
21 #elif $name.is_of_type("mothur.count_table"):
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
22 count=name.dat,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
23 #end if
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
24 #if $group:
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
25 group=group.dat,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
26 #end if
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
27 diffs=$diffs,
1
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
28 match=$match,
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
29 mismatch=$mismatch,
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
30 gapopen=$gapopen,
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
31 gapextend=$gapextend,
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
32 topdown=$topdown,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
33 processors='\${GALAXY_SLOTS:-8}'
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
34 )'
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
35 | sed 's/ //g' ## mothur trips over whitespace
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
36 | mothur
1
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
37 | tee mothur.out.log &&
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
38
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
39 if [ -f fasta.precluster.map ]; then mv fasta.precluster.map fasta.precluster.fasta.map; fi
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
40 ]]></command>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
41 <inputs>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
42 <param name="fasta" type="data" format="fasta" label="fasta - Sequence Fasta"/>
1
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
43 <param name="name" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Name reference"/>
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
44 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
45 <param name="diffs" type="integer" value="1" min="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 1)"/>
1
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
46 <param name="match" type="integer" value="1" label="match - reward for a match (default 1)"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
47 <param name="mismatch" type="integer" value="-1" label="mismatch - penalty for a mismatch (default -1)"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
48 <param name="gapopen" type="integer" value="-2" label="gapopen - penalty for opening a gap (default -2)"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
49 <param name="gapextend" type="integer" value="-1" label="gapextend - penalty for extending a gap (default -1)"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
50 <param name="topdown" type="boolean" truevalue="true" falsevalue="false" checked="true" label="topdown" help="cluster from largest abundance to smallest or vice versa. Default=Yes, meaning largest to smallest"/>
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
51 </inputs>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
52 <outputs>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
53 <expand macro="logfile-output"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
54 <data name="fasta_out" format_source="fasta" from_work_dir="fasta*.precluster.dat" label="${tool.name} on ${on_string}: precluster.fasta"/>
1
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
55 <data name="names_out" format="mothur.names" from_work_dir="fasta*.precluster.names" label="${tool.name} on ${on_string}: precluster.names">
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
56 <filter>name.ext != "mothur.count_table"</filter>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
57 </data>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
58 <data name="count_out" format="mothur.count_table" from_work_dir="fasta*.precluster.count_table" label="${tool.name} on ${on_string}: precluster.count_table">
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
59 <filter>name.ext == "mothur.count_table"</filter>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
60 </data>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
61 <collection name="map_out" type="list" label="${tool.name} on ${on_string}: precluster.map">
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
62 <discover_datasets pattern="fasta\.precluster\.(?P&lt;designation&gt;.*)\.map" format="tabular"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
63 </collection>
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
64 </outputs>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
65 <tests>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
66 <test><!-- test with fasta and names file -->
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
67 <param name="fasta" value="amazon.fasta_head" ftype="fasta"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
68 <param name="name" value="amazon.head.names" ftype="mothur.names"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
69 <output name="fasta_out" md5="d5d37ace0f2a5c020edd0aa9eb7aca9b" ftype="fasta"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
70 <output name="names_out" md5="51090fe5e111920ec1003c2073532d96" ftype="mothur.names"/>
1
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
71 <output_collection name="map_out" count="1">
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
72 <element name="fasta" md5="c2ca7b0d45aa3881c7bd5cb8a44c853b" ftype="tabular"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
73 </output_collection>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
74 <expand macro="logfile-test"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
75 </test>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
76 <test><!-- test with fasta and count table -->
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
77 <param name="fasta" value="amazon.fasta_head" ftype="fasta"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
78 <param name="name" value="amazon.count_table" ftype="mothur.count_table"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
79 <output name="fasta_out" md5="d5d37ace0f2a5c020edd0aa9eb7aca9b" ftype="fasta"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
80 <output name="count_out" md5="9831e271b9a96f91ad700f84aeed03a5" ftype="mothur.count_table"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
81 <output_collection name="map_out" count="1">
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
82 <element name="fasta" md5="c2ca7b0d45aa3881c7bd5cb8a44c853b" ftype="tabular"/>
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
83 </output_collection>
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
84 <expand macro="logfile-test"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
85 </test>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
86 </tests>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
87 <help>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
88 <![CDATA[
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
89
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
90 @MOTHUR_OVERVIEW@
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
91
1
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
92 **Command Documentation**
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
93
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
94 The pre.cluster_ command implements a pseudo-single linkage algorithm with the goal of removing sequences that are likely due to pyrosequencing errors. The basic idea is that abundant sequences are more likely to generate erroneous sequences than rare sequences. With that in mind, the algorithm proceeds by ranking sequences in order of their abundance. Then we walk through the list of sequences looking for rarer sequences that are within some threshold of the original sequence. Those that are within the threshold are merged with the larger sequence. The original Huse method performs this task on a distance matrix, whereas we do it based on the original sequences. The advantage of our approach is that the algorithm works on aligned sequences instead of a distance matrix. This is advantageous because by pre-clustering you remove a large number of sequences making the distance calculation much faster.
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
95
1
e277ab688993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
96 .. _pre.cluster: https://www.mothur.org/wiki/Pre.cluster
0
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
97
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
98 v1.24.0: Updated to mothur 1.33, added count and topdown parameter
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
99 ]]>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
100 </help>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
101 <expand macro="citations"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
102 </tool>