Mercurial > repos > iuc > mothur_consensus_seqs

comparison consensus.seqs.xml @ 3:05195067dd2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:43:32 -0500
parents fb0eb9393fa8
children e26da66f2ad8
comparison
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2:e493ad56afa2 3:05195067dd2e
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 "$name" name.dat && 14 ln -s '$name' name.dat &&
15 ln -s "$count" count.dat && 15 ln -s '$count' count.dat &&
16 #if $perotu.use == "yes": 16 #if $perotu.use == "yes":
17 ln -s "$perotu.otu" perotu.otu.dat && 17 ln -s '$perotu.otu' perotu.otu.dat &&
18 #end if
19
20 echo 'consensus.seqs(
21 fasta=fasta.dat
22 #if $name:
23 ,name=name.dat
24 #end if
25 #if $cutoff:
26 ,cutoff=$cutoff
27 #end if
28 #if $perotu.use == "yes":
29 ,list=perotu.otu.dat
30 #if $perotu.label:
31 ,label=${ str($perotu.label).replace(",","-") }
18 #end if 32 #end if
19 33 #end if
20 echo 'consensus.seqs( 34 #if $count:
21 fasta=fasta.dat 35 ,count=count.dat
22 #if $name: 36 #end if
23 ,name=name.dat 37 )'
24 #end if 38 | sed 's/ //g' ## mothur trips over whitespace
25 #if $cutoff: 39 | mothur
26 ,cutoff=$cutoff 40 | tee mothur.out.log
27 #end if
28 #if $perotu.use == "yes":
29 ,list=perotu.otu.dat
30 #if $perotu.label:
31 ,label=${ str($perotu.label).replace(",","-") }
32 #end if
33 #end if
34 #if $count:
35 ,count=count.dat
36 #end if
37 )'
38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur
40 | tee mothur.out.log
41 ]]></command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 <param name="fasta" type="data" format="mothur.align" label="fasta - Sequences to Bin" help="Sequences must be aligned"/> 43 <param name="fasta" type="data" format="mothur.align" label="fasta - Sequences to Bin" help="Sequences must be aligned"/>
44 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 44 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
45 <conditional name="perotu"> 45 <conditional name="perotu">
53 <expand macro="labeloptions"/> 53 <expand macro="labeloptions"/>
54 </param> 54 </param>
55 </when> 55 </when>
56 <when value="no"/> 56 <when value="no"/>
57 </conditional> 57 </conditional>
58 <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base" help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/> 58 <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base"
59 help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/>
59 <param name="count" type="data" format="mothur.count_table" optional="true" label="Count - a count table" help="this file can be generated by count.seqs"/> 60 <param name="count" type="data" format="mothur.count_table" optional="true" label="Count - a count table" help="this file can be generated by count.seqs"/>
60 </inputs> 61 </inputs>
61 <outputs> 62 <outputs>
62 <expand macro="logfile-output"/> 63 <expand macro="logfile-output"/>
63 <data name="summary" format="tabular" from_work_dir="fasta*.cons.summary" label="${tool.name} on ${on_string}: cons.summary"> 64 <data name="summary" format="tabular" from_work_dir="fasta*.cons.summary" label="${tool.name} on ${on_string}: cons.summary">
102 <element name="0.30" md5="d595234c6018dfcc1465e59d35d59205" ftype="tabular"/> 103 <element name="0.30" md5="d595234c6018dfcc1465e59d35d59205" ftype="tabular"/>
103 </output_collection> 104 </output_collection>
104 <expand macro="logfile-test"/> 105 <expand macro="logfile-test"/>
105 </test> 106 </test>
106 </tests> 107 </tests>
107 <help> 108 <help><![CDATA[
108 <![CDATA[
109 109
110 @MOTHUR_OVERVIEW@ 110 @MOTHUR_OVERVIEW@
111 111
112 **Command Documentation** 112 **Command Documentation**
113 113
114 The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned. 114 The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.
115 115
116 .. _consensus.seqs: https://www.mothur.org/wiki/Consensus.seqs 116 .. _consensus.seqs: https://www.mothur.org/wiki/Consensus.seqs
117 ]]> 117
118 </help> 118 ]]></help>
119 <expand macro="citations"/> 119 <expand macro="citations"/>
120 </tool> 120 </tool>