Mercurial > repos > iuc > mothur_chimera_check
comparison chimera.check.xml @ 0:8e874c18a298 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 05:07:56 -0400 |
parents | |
children | 37bd32018025 |
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-1:000000000000 | 0:8e874c18a298 |
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1 <tool profile="16.07" id="mothur_chimera_check" name="Chimera.check" 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 "$fasta" fasta.dat && | |
14 ln -s "$alignment.template" alignment.template.dat && | |
15 #if $svg.gen == "yes": | |
16 ln -s "$svg.name" svg.name.dat && | |
17 #end if | |
18 | |
19 echo 'chimera.check( | |
20 fasta=fasta.dat, | |
21 reference=alignment.template.dat, | |
22 #if $svg.gen == "yes": | |
23 svg=yes, | |
24 name=svg.name.dat, | |
25 #end if | |
26 increment=$increment, | |
27 ksize=$ksize, | |
28 processors='\${GALAXY_SLOTS:-8}' | |
29 )' | |
30 | sed 's/ //g' ## mothur trips over whitespace | |
31 | mothur | |
32 | tee mothur.out.log | |
33 ]]></command> | |
34 <inputs> | |
35 <param name="fasta" type="data" format="mothur.align" argument="fasta" label="fasta - Candiate Aligned Sequences"/> | |
36 <conditional name="alignment"> | |
37 <param name="source" type="select" label="Select Reference Template from" help=""> | |
38 <option value="hist">History</option> | |
39 <option value="ref">Cached Reference</option> | |
40 </param> | |
41 <when value="ref"> | |
42 <param name="template" type="select" argument="reference" label="reference - Select an alignment database" help=""> | |
43 <options from_data_table="mothur_aligndb"> | |
44 </options> | |
45 </param> | |
46 </when> | |
47 <when value="hist"> | |
48 <param name="template" type="data" format="fasta" argument="reference" label="reference - Reference to align with" help=""/> | |
49 </when> | |
50 </conditional> | |
51 <param name="ksize" type="integer" value="7" argument="ksize" label="ksize - kmer length to determine differences between sequence fragments (uses default if < 1)"/> | |
52 <param name="increment" type="integer" value="10" argument="increment" label="increment - Increment for window slide on each iteration (uses default if < 1)" help="Default is 10, but you may set it up to sequence length minus twice the window."/> | |
53 <conditional name="svg"> | |
54 <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help=""> | |
55 <option value="no" selected="true">No</option> | |
56 <option value="yes">Yes</option> | |
57 </param> | |
58 <when value="no"/> | |
59 <when value="yes"> | |
60 <param name="name" type="data" format="mothur.names" optional="true" argument="name" label="name - Names of queries for which to generate SVG plot"/> | |
61 </when> | |
62 </conditional> | |
63 </inputs> | |
64 <outputs> | |
65 <expand macro="logfile-output"/> | |
66 <data name="out_file" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/> | |
67 <collection name="images" type="list" label="${tool.name} on ${on_string}: SVG images"> | |
68 <discover_datasets pattern="(?P<designation>.*)\.chimeracheck\.svg"/> | |
69 <filter>svg['gen'] == 'yes'</filter> | |
70 </collection> | |
71 </outputs> | |
72 <tests> | |
73 <test> | |
74 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> | |
75 <param name="source" value="hist"/> | |
76 <param name="template" value="HMP_MOCK.v35.align"/> | |
77 <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> | |
78 <expand macro="logfile-test"/> | |
79 </test> | |
80 <test> | |
81 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> | |
82 <param name="source" value="hist"/> | |
83 <param name="template" value="HMP_MOCK.v35.align"/> | |
84 <param name="gen" value="yes"/> | |
85 <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny"/> | |
86 <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> | |
87 <output_collection name="images" count="2"> | |
88 <element name="M00967_43_000000000-A3JHG_1_1101_14010_4122" file="M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg"/> | |
89 <element name="M00967_43_000000000-A3JHG_1_1101_13293_4703" md5="0d99dc17c183dab4efc75c697060a9a5"/> | |
90 </output_collection> | |
91 <expand macro="logfile-test"/> | |
92 </test> | |
93 </tests> | |
94 <help> | |
95 <![CDATA[ | |
96 | |
97 @MOTHUR_OVERVIEW@ | |
98 | |
99 **Command Documentation** | |
100 | |
101 The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows. | |
102 | |
103 Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced. | |
104 | |
105 .. _chimera.check: https://www.mothur.org/wiki/Chimera.check | |
106 | |
107 ]]> | |
108 </help> | |
109 <expand macro="citations"/> | |
110 </tool> |