Mercurial > repos > iuc > mothur_chimera_check
comparison chimera.check.xml @ 2:37bd32018025 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:20:22 -0400 |
parents | 8e874c18a298 |
children |
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1:a1a24fae6f39 | 2:37bd32018025 |
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5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
9 <command><![CDATA[ | 9 <command><![CDATA[ |
10 @SHELL_OPTIONS@ | 10 @SHELL_OPTIONS@ |
11 | 11 |
12 ## create symlinks to input datasets | 12 ## create symlinks to input datasets |
13 ln -s "$fasta" fasta.dat && | 13 ln -s '$fasta' fasta.dat && |
14 ln -s "$alignment.template" alignment.template.dat && | 14 ln -s '$alignment.reference' alignment.reference.dat && |
15 #if $svg.gen == "yes": | 15 #if $svg_cond.svg == "yes": |
16 ln -s "$svg.name" svg.name.dat && | 16 ln -s '$svg_cond.name' svg.name.dat && |
17 #end if | 17 #end if |
18 | 18 |
19 echo 'chimera.check( | 19 echo 'chimera.check( |
20 fasta=fasta.dat, | 20 fasta=fasta.dat, |
21 reference=alignment.template.dat, | 21 reference=alignment.reference.dat, |
22 #if $svg.gen == "yes": | 22 #if $svg_cond.svg == "yes": |
23 svg=yes, | 23 svg=yes, |
24 name=svg.name.dat, | 24 name=svg.name.dat, |
25 #end if | 25 #end if |
26 increment=$increment, | 26 increment=$increment, |
27 ksize=$ksize, | 27 ksize=$ksize, |
28 processors='\${GALAXY_SLOTS:-8}' | 28 processors='\${GALAXY_SLOTS:-8}' |
29 )' | 29 )' |
30 | sed 's/ //g' ## mothur trips over whitespace | 30 | sed 's/ //g' ## mothur trips over whitespace |
31 | mothur | 31 | mothur |
32 | tee mothur.out.log | 32 | tee mothur.out.log |
33 ]]></command> | 33 ]]></command> |
34 <inputs> | 34 <inputs> |
35 <param name="fasta" type="data" format="mothur.align" argument="fasta" label="fasta - Candiate Aligned Sequences"/> | 35 <param argument="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/> |
36 <conditional name="alignment"> | 36 <conditional name="alignment"> |
37 <param name="source" type="select" label="Select Reference Template from" help=""> | 37 <param name="source" type="select" label="Select Reference Template from"> |
38 <option value="hist">History</option> | 38 <option value="hist">History</option> |
39 <option value="ref">Cached Reference</option> | 39 <option value="ref">Cached Reference</option> |
40 </param> | 40 </param> |
41 <when value="ref"> | 41 <when value="ref"> |
42 <param name="template" type="select" argument="reference" label="reference - Select an alignment database" help=""> | 42 <param argument="reference" type="select" label="reference - Select an alignment database"> |
43 <options from_data_table="mothur_aligndb"> | 43 <options from_data_table="mothur_aligndb"/> |
44 </options> | |
45 </param> | 44 </param> |
46 </when> | 45 </when> |
47 <when value="hist"> | 46 <when value="hist"> |
48 <param name="template" type="data" format="fasta" argument="reference" label="reference - Reference to align with" help=""/> | 47 <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/> |
49 </when> | 48 </when> |
50 </conditional> | 49 </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)"/> | 50 <param argument="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments" |
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."/> | 51 help="uses default if < 1"/> |
53 <conditional name="svg"> | 52 <param argument="increment" type="integer" value="10" label="increment - Increment for window slide on each iteration" |
54 <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help=""> | 53 help="Default is 10, but you may set it up to sequence length minus twice the window."/> |
54 <conditional name="svg_cond"> | |
55 <param argument="svg" type="select" label="svg - Generate a SVG plot for each query sequence"> | |
55 <option value="no" selected="true">No</option> | 56 <option value="no" selected="true">No</option> |
56 <option value="yes">Yes</option> | 57 <option value="yes">Yes</option> |
57 </param> | 58 </param> |
58 <when value="no"/> | 59 <when value="no"/> |
59 <when value="yes"> | 60 <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 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Names of queries for which to generate SVG plot"/> |
61 </when> | 62 </when> |
62 </conditional> | 63 </conditional> |
64 <expand macro="param-savelog"/> | |
63 </inputs> | 65 </inputs> |
64 <outputs> | 66 <outputs> |
65 <expand macro="logfile-output"/> | 67 <expand macro="logfile-output"/> |
66 <data name="out_file" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/> | 68 <data name="chimeracheck.chimeras" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/> |
67 <collection name="images" type="list" label="${tool.name} on ${on_string}: SVG images"> | 69 <collection name="images" type="list" label="${tool.name} on ${on_string}: SVG images"> |
68 <discover_datasets pattern="(?P<designation>.*)\.chimeracheck\.svg"/> | 70 <discover_datasets pattern="(?P<designation>.*)\.chimeracheck\.svg"/> |
69 <filter>svg['gen'] == 'yes'</filter> | 71 <filter>svg['gen'] == 'yes'</filter> |
70 </collection> | 72 </collection> |
71 </outputs> | 73 </outputs> |
72 <tests> | 74 <tests> |
73 <test> | 75 <test> |
74 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> | 76 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> |
75 <param name="source" value="hist"/> | 77 <param name="source" value="hist"/> |
76 <param name="template" value="HMP_MOCK.v35.align"/> | 78 <param name="reference" value="HMP_MOCK.v35.align"/> |
77 <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> | 79 <output name="chimeracheck.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> |
80 <param name="savelog" value="true"/> | |
78 <expand macro="logfile-test"/> | 81 <expand macro="logfile-test"/> |
79 </test> | 82 </test> |
80 <test> | 83 <test> |
81 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> | 84 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> |
82 <param name="source" value="hist"/> | 85 <param name="source" value="hist"/> |
83 <param name="template" value="HMP_MOCK.v35.align"/> | 86 <param name="reference" value="HMP_MOCK.v35.align"/> |
84 <param name="gen" value="yes"/> | 87 <param name="svg" value="yes"/> |
85 <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny"/> | 88 <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"/> | 89 <output name="chimeracheck.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> |
87 <output_collection name="images" count="2"> | 90 <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"/> | 91 <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"/> | 92 <element name="M00967_43_000000000-A3JHG_1_1101_13293_4703" md5="0d99dc17c183dab4efc75c697060a9a5"/> |
90 </output_collection> | 93 </output_collection> |
94 <param name="savelog" value="true"/> | |
91 <expand macro="logfile-test"/> | 95 <expand macro="logfile-test"/> |
92 </test> | 96 </test> |
93 </tests> | 97 </tests> |
94 <help> | 98 <help><![CDATA[ |
95 <![CDATA[ | |
96 | 99 |
97 @MOTHUR_OVERVIEW@ | 100 @MOTHUR_OVERVIEW@ |
98 | 101 |
99 **Command Documentation** | 102 **Command Documentation** |
100 | 103 |
102 | 105 |
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. | 106 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 | 107 |
105 .. _chimera.check: https://www.mothur.org/wiki/Chimera.check | 108 .. _chimera.check: https://www.mothur.org/wiki/Chimera.check |
106 | 109 |
107 ]]> | 110 ]]></help> |
108 </help> | |
109 <expand macro="citations"/> | 111 <expand macro="citations"/> |
110 </tool> | 112 </tool> |