Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/chimera.slayer.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
parents | 3202a38e44d9 |
children | e990ac8a0f58 |
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0:3202a38e44d9 | 1:fcc0778f6987 |
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1 <tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.15.0"> | 1 <tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.16.0"> |
2 <description>Find putative chimeras using slayer</description> | 2 <description>Find putative chimeras using slayer</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='chimera.slayer' | 5 --cmd='chimera.slayer' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.slayer\.chimeras$:'$out_file,'^\S+\.slayer\.accnos$:'$out_accnos | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.slayer\.chimeras$:'$out_file,'^\S+\.slayer\.accnos$:'$out_accnos |
7 --outputdir='$logfile.extra_files_path' | 7 --outputdir='$logfile.extra_files_path' |
8 --tmpdir='${logfile.extra_files_path}/input' | 8 --tmpdir='${logfile.extra_files_path}/input' |
9 --fasta=$fasta | 9 --fasta=$fasta |
10 --template=$alignment.template | 10 #if $alignment.source == 'self': |
11 --template='self' | |
12 #if $alignment.name.__str__ != "None" and len($alignment.name.__str__) > 0: | |
13 --name=$alignment.name | |
14 #end if | |
15 #else: | |
16 --template=$alignment.template | |
17 #end if | |
11 #if $options.setby == 'user': | 18 #if $options.setby == 'user': |
12 --search=$options.search | 19 --search=$options.search |
13 --window=$options.window | 20 --window=$options.window |
14 --increment=$options.increment | 21 --increment=$options.increment |
15 --match=$options.match | 22 --match=$options.match |
20 --mincov=$options.mincov | 27 --mincov=$options.mincov |
21 --iters=$options.iters | 28 --iters=$options.iters |
22 --minbs=$options.minbs | 29 --minbs=$options.minbs |
23 --minsnp=$options.minsnp | 30 --minsnp=$options.minsnp |
24 --divergence=$options.divergence | 31 --divergence=$options.divergence |
32 $options.trim | |
25 #end if | 33 #end if |
34 --processors=2 | |
26 </command> | 35 </command> |
27 <inputs> | 36 <inputs> |
28 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> | 37 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> |
29 <conditional name="alignment"> | 38 <conditional name="alignment"> |
30 <param name="source" type="select" label="Select Template from" help=""> | 39 <param name="source" type="select" label="Select Template from" help=""> |
31 <option value="hist">History</option> | 40 <option value="hist">History</option> |
32 <option value="ref">Cached Reference</option> | 41 <option value="ref">Cached Reference</option> |
42 <option value="self">Self - Use abundant sequences from the input Candiate Sequences fasta </option> | |
33 </param> | 43 </param> |
34 <when value="ref"> | 44 <when value="ref"> |
35 <param name="template" type="select" label="template - Select an alignment database " help=""> | 45 <param name="template" type="select" label="template - Select an alignment database " help=""> |
36 <options from_file="mothur_aligndb.loc"> | 46 <options from_file="mothur_aligndb.loc"> |
37 <column name="name" index="0" /> | 47 <column name="name" index="0" /> |
39 </options> | 49 </options> |
40 </param> | 50 </param> |
41 </when> | 51 </when> |
42 <when value="hist"> | 52 <when value="hist"> |
43 <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/> | 53 <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/> |
54 </when> | |
55 <when value="self"> | |
56 <param name="name" type="data" format="names" optional="true" label="names - Sequences Names"/> | |
44 </when> | 57 </when> |
45 </conditional> | 58 </conditional> |
46 <conditional name="options"> | 59 <conditional name="options"> |
47 <param name="setby" type="select" label="Slayer Options" help=""> | 60 <param name="setby" type="select" label="Slayer Options" help=""> |
48 <option value="default">Use default settings</option> | 61 <option value="default">Use default settings</option> |
65 <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in template and the query (default 70)"/> | 78 <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in template and the query (default 70)"/> |
66 <param name="iters" type="integer" value="100" label="iters - Number of bootstrap iterations to try (default 100)"/> | 79 <param name="iters" type="integer" value="100" label="iters - Number of bootstrap iterations to try (default 100)"/> |
67 <param name="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/> | 80 <param name="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/> |
68 <param name="minsnp" type="integer" value="100" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 100)"/> | 81 <param name="minsnp" type="integer" value="100" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 100)"/> |
69 <param name="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/> | 82 <param name="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/> |
83 <param name="trim" type="boolean" truevalue="--trim=True" falsevalue="" checked="false" label="trim - include chimeric sequences trimmed to their longest peice" /> | |
70 </when> | 84 </when> |
71 </conditional> | 85 </conditional> |
72 </inputs> | 86 </inputs> |
73 <outputs> | 87 <outputs> |
74 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 88 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |