Mercurial > repos > iuc > mothur_cluster_fragments

comparison cluster.fragments.xml @ 2:19bb0a1a459e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:22:06 -0400
parents 145595c55727
children 7b96c990a457
comparison
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1:978cdd9b48d3 2:19bb0a1a459e
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 ln -s "$names" names.dat && 14 ln -s '$names' names.dat &&
15 ln -s "$count" count.dat && 15 ln -s '$count' count.dat &&
16 16
17 echo 'cluster.fragments( 17 echo 'cluster.fragments(
18 fasta=fasta.dat, 18 fasta=fasta.dat,
19 diffs=$diffs, 19 diffs=$diffs,
20 percent=$percent, 20 percent=$percent,
21 #if $count: 21 #if $count:
22 count=count.dat, 22 count=count.dat,
23 #end if 23 #end if
24 name=names.dat 24 name=names.dat
25 )' 25 )'
26 | sed 's/ //g' ## mothur trips over whitespace 26 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur 27 | mothur
28 | tee mothur.out.log 28 | tee mothur.out.log
29 ]]></command> 29 ]]></command>
30 <inputs> 30 <inputs>
31 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> 31 <param argument="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
32 <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 32 <param argument="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
33 <param name="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)" min="0"/> 33 <param argument="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)" min="0"/>
34 <param name="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" min="0" max="100" 34 <param argument="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" min="0" max="100"
35 help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge."/> 35 help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less
36 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 36 than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like:
37 If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge."/>
38 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
39 <expand macro="param-savelog"/>
37 </inputs> 40 </inputs>
38 <outputs> 41 <outputs>
39 <expand macro="logfile-output"/> 42 <expand macro="logfile-output"/>
40 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.fragclust.fasta" label="${tool.name} on ${on_string}: fasta"/> 43 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.fragclust.fasta" label="${tool.name} on ${on_string}: fasta"/>
41 <data name="out_names" format="mothur.names" from_work_dir="fasta*.fragclust.names" label="${tool.name} on ${on_string}: names"/> 44 <data name="out_names" format="mothur.names" from_work_dir="fasta*.fragclust.names" label="${tool.name} on ${on_string}: names"/>
44 <test> 47 <test>
45 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 48 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
46 <param name="names" value="amazon1.names" ftype="mothur.names"/> 49 <param name="names" value="amazon1.names" ftype="mothur.names"/>
47 <output name="out_fasta" file="amazon.fragclust.fasta" ftype="fasta"/> 50 <output name="out_fasta" file="amazon.fragclust.fasta" ftype="fasta"/>
48 <output name="out_names" file="amazon.fragclust.names" ftype="mothur.names"/> 51 <output name="out_names" file="amazon.fragclust.names" ftype="mothur.names"/>
52 <param name="savelog" value="true"/>
49 <expand macro="logfile-test"/> 53 <expand macro="logfile-test"/>
50 </test> 54 </test>
51 </tests> 55 </tests>
52 <help> 56 <help><![CDATA[
53 <![CDATA[
54 57
55 @MOTHUR_OVERVIEW@ 58 @MOTHUR_OVERVIEW@
56 59
57 **Command Documentation** 60 **Command Documentation**
58 61
60 63
61 .. _cluster.fragments: https://www.mothur.org/wiki/Cluster.fragments 64 .. _cluster.fragments: https://www.mothur.org/wiki/Cluster.fragments
62 65
63 v1.21: Updated to Mothur 1.33. Added count parameter. 66 v1.21: Updated to Mothur 1.33. Added count parameter.
64 67
65 ]]> 68 ]]></help>
66 </help>
67 <expand macro="citations"/> 69 <expand macro="citations"/>
68 </tool> 70 </tool>