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comparison chimera.check.xml @ 0:8e874c18a298 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:07:56 -0400
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children 37bd32018025
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-1:000000000000 0:8e874c18a298
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=$ksize,
28 processors='\${GALAXY_SLOTS:-8}'
29 )'
30 | sed 's/ //g' ## mothur trips over whitespace
31 | mothur
32 | tee mothur.out.log
33 ]]></command>
34 <inputs>
35 <param name="fasta" type="data" format="mothur.align" argument="fasta" label="fasta - Candiate Aligned Sequences"/>
36 <conditional name="alignment">
37 <param name="source" type="select" label="Select Reference Template from" help="">
38 <option value="hist">History</option>
39 <option value="ref">Cached Reference</option>
40 </param>
41 <when value="ref">
42 <param name="template" type="select" argument="reference" label="reference - Select an alignment database" help="">
43 <options from_data_table="mothur_aligndb">
44 </options>
45 </param>
46 </when>
47 <when value="hist">
48 <param name="template" type="data" format="fasta" argument="reference" label="reference - Reference to align with" help=""/>
49 </when>
50 </conditional>
51 <param name="ksize" type="integer" value="7" argument="ksize" label="ksize - kmer length to determine differences between sequence fragments (uses default if &lt; 1)"/>
52 <param name="increment" type="integer" value="10" argument="increment" label="increment - Increment for window slide on each iteration (uses default if &lt; 1)" help="Default is 10, but you may set it up to sequence length minus twice the window."/>
53 <conditional name="svg">
54 <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help="">
55 <option value="no" selected="true">No</option>
56 <option value="yes">Yes</option>
57 </param>
58 <when value="no"/>
59 <when value="yes">
60 <param name="name" type="data" format="mothur.names" optional="true" argument="name" label="name - Names of queries for which to generate SVG plot"/>
61 </when>
62 </conditional>
63 </inputs>
64 <outputs>
65 <expand macro="logfile-output"/>
66 <data name="out_file" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${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&lt;designation&gt;.*)\.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>