Mercurial > repos > iuc > mothur_chimera_check

comparison chimera.check.xml @ 2:37bd32018025 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:20:22 -0400
parents 8e874c18a298
children
comparison
equal deleted inserted replaced
1:a1a24fae6f39 2:37bd32018025
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 &lt; 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 &lt; 1)" help="Default is 10, but you may set it up to sequence length minus twice the window."/> 51 help="uses default if &lt; 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&lt;designation&gt;.*)\.chimeracheck\.svg"/> 70 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.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>