Mercurial > repos > iuc > mothur_primer_design

comparison primer.design.xml @ 2:fb7c0871d8af 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 22:03:11 -0400
parents 79490c77c27f
children 6e8cdd7e6825
comparison
equal deleted inserted replaced
1:7c3df0f11815 2:fb7c0871d8af
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 "$otu" otu.dat && 14 ln -s '$otu' otu.dat &&
15 ln -s "$name" name.dat && 15 ln -s '$name' name.dat &&
16 ln -s "$count" count.dat && 16 ln -s '$count' count.dat &&
17 17
18 echo 'primer.design( 18 echo 'primer.design(
19 fasta=fasta.dat, 19 fasta=fasta.dat,
20 list=otu.dat, 20 list=otu.dat,
21 #if $label: 21 #if $label:
22 label=$label, 22 label=$label,
23 #end if 23 #end if
24 otulabel=$otulabel, 24 otulabel=$otulabel,
25 #if $name: 25 #if $name:
26 name=name.dat, 26 name=name.dat,
27 #end if 27 #end if
28 #if $count: 28 #if $count:
29 count=count.dat, 29 count=count.dat,
30 #end if 30 #end if
31 #if $cutoff: 31 #if $cutoff:
32 cutoff=$cutoff, 32 cutoff=$cutoff,
33 #end if 33 #end if
34 #if $mintm: 34 #if $mintm:
35 mintm=$mintm, 35 mintm=$mintm,
36 #end if 36 #end if
37 #if $maxtm: 37 #if $maxtm:
38 maxtm=$maxtm, 38 maxtm=$maxtm,
39 #end if 39 #end if
40 pdiffs=$pdiffs, 40 pdiffs=$pdiffs,
41 length=$length, 41 length=$length,
42 processors='\${GALAXY_SLOTS:-8}' 42 processors='\${GALAXY_SLOTS:-8}'
43 )' 43 )'
44 | sed 's/ //g' ## mothur trips over whitespace 44 | sed 's/ //g' ## mothur trips over whitespace
45 | mothur 45 | mothur
46 | tee mothur.out.log 46 | tee mothur.out.log
47 ]]></command> 47 ]]></command>
48 <inputs> 48 <inputs>
49 <param name="fasta" type="data" format="mothur.align" label="fasta - provide aligned fasta file"/> 49 <param name="fasta" type="data" format="mothur.align" label="fasta - provide aligned fasta file"/>
50 <param name="otu" type="data" format="mothur.list" label="list - OTU list file"/> 50 <param name="otu" type="data" format="mothur.list" label="list - OTU list file"/>
51 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels" help="If none selected, the first label in your file will be used"> 51 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels" help="If none selected, the first label in your file will be used">
61 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - specify the number of differences allowed in the primer" help=""/> 61 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - specify the number of differences allowed in the primer" help=""/>
62 <param name="length" type="integer" value="18" min="0" label="length - indicate the length of the primer" help=""/> 62 <param name="length" type="integer" value="18" min="0" label="length - indicate the length of the primer" help=""/>
63 <param name="mintm" type="integer" value="" optional="true" label="mintm - indicate minimum melting temperature" help=""/> 63 <param name="mintm" type="integer" value="" optional="true" label="mintm - indicate minimum melting temperature" help=""/>
64 <param name="maxtm" type="integer" value="" optional="true" label="maxtm - indicate maximum melting temperature" help=""/> 64 <param name="maxtm" type="integer" value="" optional="true" label="maxtm - indicate maximum melting temperature" help=""/>
65 <param name="cutoff" type="integer" value="" optional="true" min="0" max="100" label="cutoff - set a percentage of sequences that support the base" help="For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences."/> 65 <param name="cutoff" type="integer" value="" optional="true" min="0" max="100" label="cutoff - set a percentage of sequences that support the base" help="For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences."/>
66 <expand macro="param-savelog"/>
66 </inputs> 67 </inputs>
67 <outputs> 68 <outputs>
68 <expand macro="logfile-output"/> 69 <expand macro="logfile-output"/>
69 <data name="fasta_out" format="mothur.align" from_work_dir="otu*.cons.fasta" label="${tool.name} on ${on_string}: cons.fasta"/> 70 <data name="fasta_out" format="mothur.align" from_work_dir="otu*.cons.fasta" label="${tool.name} on ${on_string}: cons.fasta"/>
70 <data name="summary_out" format="tabular" from_work_dir="otu*.primer.summary" label="${tool.name} on ${on_string}: primer.summary"/> 71 <data name="summary_out" format="tabular" from_work_dir="otu*.primer.summary" label="${tool.name} on ${on_string}: primer.summary"/>
77 <param name="otulabel" value="Otu1"/> 78 <param name="otulabel" value="Otu1"/>
78 <param name="label" value="0.30"/> 79 <param name="label" value="0.30"/>
79 <output name="fasta_out" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/> 80 <output name="fasta_out" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/>
80 <output name="summary_out" md5="8dd341c49c26c6d0f8026b34cb7bc925" ftype="tabular"/> 81 <output name="summary_out" md5="8dd341c49c26c6d0f8026b34cb7bc925" ftype="tabular"/>
81 <output name="list_out" md5="0a73804f3d48c668b4dab85c76d2c767" ftype="mothur.list"/> 82 <output name="list_out" md5="0a73804f3d48c668b4dab85c76d2c767" ftype="mothur.list"/>
83 <param name="savelog" value="true"/>
82 <expand macro="logfile-test"/> 84 <expand macro="logfile-test"/>
83 </test> 85 </test>
84 </tests> 86 </tests>
85 <help> 87 <help><![CDATA[
86 <![CDATA[
87 88
88 @MOTHUR_OVERVIEW@ 89 @MOTHUR_OVERVIEW@
89 90
90 **Command Documentation** 91 **Command Documentation**
91 92
92 The primer.design_ allows you to identify sequence fragments that are specific to particular OTUs. 93 The primer.design_ allows you to identify sequence fragments that are specific to particular OTUs.
93 94
94 .. _primer.design: https://www.mothur.org/wiki/Primer.design 95 .. _primer.design: https://www.mothur.org/wiki/Primer.design
95 96
96 ]]> 97 ]]></help>
97 </help>
98 <citations> 98 <citations>
99 <citation type="doi">10.1128/AEM.01541-09</citation> 99 <citation type="doi">10.1128/AEM.01541-09</citation>
100 </citations> 100 </citations>
101 </tool> 101 </tool>