Mercurial > repos > iuc > mothur_consensus_seqs

comparison consensus.seqs.xml @ 2:4f4de4518aca 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 21:59:24 -0400
parents 82a5c9700e76
children
comparison
equal deleted inserted replaced
1:094f184f5b84 2:4f4de4518aca
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"/>
61 <expand macro="param-savelog"/>
60 </inputs> 62 </inputs>
61 <outputs> 63 <outputs>
62 <expand macro="logfile-output"/> 64 <expand macro="logfile-output"/>
63 <data name="summary" format="tabular" from_work_dir="fasta*.cons.summary" label="${tool.name} on ${on_string}: cons.summary"> 65 <data name="summary" format="tabular" from_work_dir="fasta*.cons.summary" label="${tool.name} on ${on_string}: cons.summary">
64 <filter>perotu['use'] == 'no'</filter> 66 <filter>perotu['use'] == 'no'</filter>
82 <tests> 84 <tests>
83 <test><!-- test with default values --> 85 <test><!-- test with default values -->
84 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 86 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
85 <output name="summary" md5="61a0e170a8b881135421afd0cea8305a" ftype="tabular"/> 87 <output name="summary" md5="61a0e170a8b881135421afd0cea8305a" ftype="tabular"/>
86 <output name="cons_fasta" md5="82f3475b61f240eba09597a409364c04" ftype="mothur.align"/> 88 <output name="cons_fasta" md5="82f3475b61f240eba09597a409364c04" ftype="mothur.align"/>
89 <param name="savelog" value="true"/>
87 <expand macro="logfile-test"/> 90 <expand macro="logfile-test"/>
88 </test> 91 </test>
89 <test><!-- test with list file --> 92 <test><!-- test with list file -->
90 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 93 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
91 <param name="use" value="yes"/> 94 <param name="use" value="yes"/>
99 <element name="0.30" md5="9de4f7e774e0c16eaf7cf6ffbba9d475" ftype="mothur.names"/> 102 <element name="0.30" md5="9de4f7e774e0c16eaf7cf6ffbba9d475" ftype="mothur.names"/>
100 </output_collection> 103 </output_collection>
101 <output_collection name="consensussummaries" count="3"> 104 <output_collection name="consensussummaries" count="3">
102 <element name="0.30" md5="d595234c6018dfcc1465e59d35d59205" ftype="tabular"/> 105 <element name="0.30" md5="d595234c6018dfcc1465e59d35d59205" ftype="tabular"/>
103 </output_collection> 106 </output_collection>
107 <param name="savelog" value="true"/>
104 <expand macro="logfile-test"/> 108 <expand macro="logfile-test"/>
105 </test> 109 </test>
106 </tests> 110 </tests>
107 <help> 111 <help><![CDATA[
108 <![CDATA[
109 112
110 @MOTHUR_OVERVIEW@ 113 @MOTHUR_OVERVIEW@
111 114
112 **Command Documentation** 115 **Command Documentation**
113 116
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. 117 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.
115 118
116 .. _consensus.seqs: https://www.mothur.org/wiki/Consensus.seqs 119 .. _consensus.seqs: https://www.mothur.org/wiki/Consensus.seqs
117 ]]> 120
118 </help> 121 ]]></help>
119 <expand macro="citations"/> 122 <expand macro="citations"/>
120 </tool> 123 </tool>