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comparison mothur/tools/mothur/chimera.perseus.xml @ 35:95d75b35e4d2

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Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author certain cat
date Fri, 31 Oct 2014 15:09:32 -0400
parents ec8df51e841a
children
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34:1be61ceb20d7 35:95d75b35e4d2
1 <tool id="mothur_chimera_perseus" name="Chimera.perseus" version="1.23.0" > 1 <tool id="mothur_chimera_perseus" name="Chimera.perseus" version="1.24.0" >
2 <description>Find putative chimeras using chimeraCheck</description> 2 <description>Find putative chimeras using chimeraCheck</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='chimera.perseus' 5 --cmd='chimera.perseus'
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file
7 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file,'^\S+\.perseus\.accnos$:'$out_accnos 7 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file,'^\S+\.perseus\.accnos$:'$out_accnos
8 --outputdir='$logfile.extra_files_path' 8 --outputdir='$logfile.extra_files_path'
9 --fasta=$fasta 9 --fasta=$fasta
10 --name=$name 10 #if isinstance($name.datatype, $__app__.datatypes_registry.get_datatype_by_extension('name').__class__):
11 --name=$name
12 #else
13 --count=$name
14 #end if
11 #if $group.__str__ != "None" and len($group.__str__) > 0: 15 #if $group.__str__ != "None" and len($group.__str__) > 0:
12 --group='$group' 16 --group='$group'
13 #end if 17 #end if
14 #if $alpha.__str__ != '': 18 #if $alpha.__str__ != '':
15 --alpha=$alpha 19 --alpha=$alpha
19 #end if 23 #end if
20 #if $cutoff.__str__ != '': 24 #if $cutoff.__str__ != '':
21 --cutoff=$cutoff 25 --cutoff=$cutoff
22 #end if 26 #end if
23 --processors=8 27 --processors=8
28 $dereplicate
24 </command> 29 </command>
25 <inputs> 30 <inputs>
26 <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/> 31 <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/>
27 <param name="name" type="data" format="names" label="name - Names "/> 32 <param name="name" type="data" format="names,count" label="name - Names or count_table"/>
28 <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/> 33 <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
29 <param name="alpha" type="float" value="-5.54" optional="true" label="alpha" help="The default is -5.54"/> 34 <param name="alpha" type="float" value="-5.54" optional="true" label="alpha" help="The default is -5.54"/>
30 <param name="beta" type="float" value="0.33" optional="true" label="beta" help="The default is 0.33"/> 35 <param name="beta" type="float" value="0.33" optional="true" label="beta" help="The default is 0.33"/>
31 <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/> 36 <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/>
37 <param name="dereplicate" type="boolean" falsevalue="" truevalue="--dereplicate=true" checked="false" label="dereplicate - remove chimeric sequences from all groups, default=f" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/>
32 </inputs> 38 </inputs>
33 <outputs> 39 <outputs>
34 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> 40 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
35 <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" /> 41 <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" />
36 <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: perseus.accnos" /> 42 <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: perseus.accnos" />
37 </outputs> 43 </outputs>
38 <requirements> 44 <requirements>
39 <requirement type="package" version="1.27">mothur</requirement> 45 <requirement type="package" version="1.33">mothur</requirement>
40 </requirements> 46 </requirements>
41 <tests> 47 <tests>
42 </tests> 48 </tests>
43 <help> 49 <help>
44 **Mothur Overview** 50 **Mothur Overview**