Mercurial > repos > iuc > mothur_chimera_perseus
comparison chimera.perseus.xml @ 0:35c11001da8b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:29:15 -0400 |
parents | |
children | 1dab91d5c40e |
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-1:000000000000 | 0:35c11001da8b |
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1 <tool profile="16.07" id="mothur_chimera_perseus" name="Chimera.perseus" version="@WRAPPER_VERSION@.0"> | |
2 <description>Find putative chimeras using chimeraCheck</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 "$fasta" fasta.dat && | |
14 ln -s "$name" name.dat && | |
15 ln -s "$group" group.dat && | |
16 | |
17 echo 'chimera.perseus( | |
18 fasta=fasta.dat, | |
19 #if $name.is_of_type("mothur.names"): | |
20 name=name.dat, | |
21 #elif $name.is_of_type("mothur.count_table"): | |
22 count=name.dat, | |
23 #end if | |
24 #if $group: | |
25 group=group.dat, | |
26 #end if | |
27 alpha=$alpha, | |
28 beta=$beta, | |
29 cutoff=$cutoff, | |
30 dereplicate=$dereplicate, | |
31 processors='\${GALAXY_SLOTS:-8}' | |
32 )' | |
33 | sed 's/ //g' ## mothur trips over whitespace | |
34 | mothur | |
35 | tee mothur.out.log | |
36 ]]></command> | |
37 <inputs> | |
38 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/> | |
39 <param name="name" type="data" format="mothur.names,mothur.count_table" label="name - Names or count_table"/> | |
40 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> | |
41 <param name="alpha" type="float" value="-5.54" label="alpha" help="The default is -5.54"/> | |
42 <param name="beta" type="float" value="0.33" label="beta" help="The default is 0.33"/> | |
43 <param name="cutoff" type="float" value="0.50" label="cutoff" help="The default is 0.50"/> | |
44 <param name="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric. default=false"/> | |
45 </inputs> | |
46 <outputs> | |
47 <expand macro="logfile-output"/> | |
48 <data name="out_chimeras" format="tabular" from_work_dir="fasta.perseus.chimeras" label="${tool.name} on ${on_string}: perseus.chimeras"/> | |
49 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.perseus.accnos" label="${tool.name} on ${on_string}: perseus.accnos"/> | |
50 </outputs> | |
51 <tests> | |
52 <test> | |
53 <param name="fasta" value="amazon.fasta" ftype="fasta"/> | |
54 <param name="name" value="amazon1.names" ftype="mothur.names"/> | |
55 <output name="out_chimeras" md5="bcd513127321a32035764a2087c23528" ftype="tabular"/> | |
56 <expand macro="logfile-test"/> | |
57 </test> | |
58 <!-- TODO: find/create test dataset with chimera present --> | |
59 </tests> | |
60 <help> | |
61 <![CDATA[ | |
62 | |
63 @MOTHUR_OVERVIEW@ | |
64 | |
65 **Command Documentation** | |
66 | |
67 The chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences. | |
68 | |
69 .. _chimera.perseus: https://www.mothur.org/wiki/Chimera.perseus | |
70 | |
71 ]]> | |
72 </help> | |
73 <expand macro="citations"/> | |
74 </tool> |