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comparison primer.design.xml @ 0:79490c77c27f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:10:09 -0400
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1 <tool profile="16.07" id="mothur_primer_design" name="Primer.design" version="@WRAPPER_VERSION@.0">
2 <description>identify sequence fragments that are specific to particular OTUs</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat &&
14 ln -s "$otu" otu.dat &&
15 ln -s "$name" name.dat &&
16 ln -s "$count" count.dat &&
17
18 echo 'primer.design(
19 fasta=fasta.dat,
20 list=otu.dat,
21 #if $label:
22 label=$label,
23 #end if
24 otulabel=$otulabel,
25 #if $name:
26 name=name.dat,
27 #end if
28 #if $count:
29 count=count.dat,
30 #end if
31 #if $cutoff:
32 cutoff=$cutoff,
33 #end if
34 #if $mintm:
35 mintm=$mintm,
36 #end if
37 #if $maxtm:
38 maxtm=$maxtm,
39 #end if
40 pdiffs=$pdiffs,
41 length=$length,
42 processors='\${GALAXY_SLOTS:-8}'
43 )'
44 | sed 's/ //g' ## mothur trips over whitespace
45 | mothur
46 | tee mothur.out.log
47 ]]></command>
48 <inputs>
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"/>
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">
52 <expand macro="labeloptions"/>
53 </param>
54 <param name="otulabel" type="select" optional="false" multiple="false" label="otulabel - choose an OTU name">
55 <options>
56 <filter type="data_meta" ref="otu" key="otulabels"/>
57 </options>
58 </param>
59 <param name="name" type="data" format="mothur.names" optional="true" label="name - names file associated with your fasta file"/>
60 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table associated with your fasta file"/>
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=""/>
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=""/>
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 </inputs>
67 <outputs>
68 <expand macro="logfile-output"/>
69 <data name="fasta_out" format="mothur.align" from_work_dir="otu*.cons.fasta" label="${tool.name} on ${on_string}: cons.fasta"/>
70 <data name="summary_out" format="tabular" from_work_dir="otu*.primer.summary" label="${tool.name} on ${on_string}: primer.summary"/>
71 <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
72 </outputs>
73 <tests>
74 <test>
75 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
76 <param name="otu" value="amazon.align_head.list" ftype="mothur.list"/>
77 <param name="otulabel" value="Otu1"/>
78 <param name="label" value="0.30"/>
79 <output name="fasta_out" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/>
80 <output name="summary_out" md5="8dd341c49c26c6d0f8026b34cb7bc925" ftype="tabular"/>
81 <output name="list_out" md5="0a73804f3d48c668b4dab85c76d2c767" ftype="mothur.list"/>
82 <expand macro="logfile-test"/>
83 </test>
84 </tests>
85 <help>
86 <![CDATA[
87
88 @MOTHUR_OVERVIEW@
89
90 **Command Documentation**
91
92 The primer.design_ allows you to identify sequence fragments that are specific to particular OTUs.
93
94 .. _primer.design: https://www.mothur.org/wiki/Primer.design
95
96 ]]>
97 </help>
98 <citations>
99 <citation type="doi">10.1128/AEM.01541-09</citation>
100 </citations>
101 </tool>