Mercurial > repos > iuc > mothur_chimera_vsearch

comparison chimera.vsearch.xml @ 0:1801019b4690 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 22:09:26 -0400
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children b4e60c1d77ac
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-1:000000000000 0:1801019b4690
1 <tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.0">
2 <description>find potential chimeric sequences using vsearch</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="2.6.0">vsearch</requirement>
8 </expand>
9 <expand macro="stdio"/>
10 <expand macro="version_command"/>
11 <command><![CDATA[
12 @SHELL_OPTIONS@
13
14 ## create symlinks to input datasets
15 ln -s '$fasta' fasta.dat &&
16 #if $template.source == "self":
17 ln -s '$template.count' template.count.dat &&
18 ln -s '$template.group' template.group.dat &&
19 #elif $template.source == "names":
20 ln -s '$template.name' template.name.dat &&
21 #else:
22 ln -s '$template.reference' template.reference.dat &&
23 #end if
24
25 echo 'chimera.vsearch(
26 fasta=fasta.dat,
27 #if $template.source == "self":
28 reference=self,
29 #if float($template.abskew) > 0:
30 abskew=$template.abskew,
31 #end if
32 #if $template.group:
33 group=template.group.dat,
34 #end if
35 #if $template.count:
36 count=template.count.dat,
37 #end if
38 #elif $template.source == "names":
39 name=template.name.dat,
40 #else:
41 reference=template.reference.dat,
42 #end if
43 minh=$minh,
44 mindiv=$mindiv,
45 xn=$xn,
46 dn=$dn,
47 dereplicate=$dereplicate,
48 mindiffs=$mindiffs,
49 processors='\${GALAXY_SLOTS:-8}'
50 )'
51 | sed 's/ //g' ## mothur trips over whitespace
52 | mothur
53 | tee mothur.out.log
54 2>&1 ## uchime component writes output to stderr
55 && cat *accnos
56 ]]></command>
57 <inputs>
58 <param argument="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Aligned Sequences"/>
59 <conditional name="template">
60 <param name="source" type="select" label="Select Reference Template from">
61 <option value="hist">History</option>
62 <option value="ref">Cached Reference</option>
63 <option value="self">Self</option>
64 <option value="names">Use a names file</option>
65 </param>
66 <when value="ref">
67 <param argument="reference" type="select" label="reference - Select an alignment database">
68 <options from_data_table="mothur_aligndb"/>
69 </param>
70 </when>
71 <when value="hist">
72 <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
73 </when>
74 <when value="self">
75 <param argument="abskew" type="float" value="1.9" label="abskew - Abundance skew" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query). Default 1.9"/>
76 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"
77 help="use the more abundant sequences from the same sample to check the query sequence"/>
78 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table"
79 help="Generated by count.seqs. When you use a count file with group info and dereplicate=T, mothur will create a count table containing seqeunces after chimeras are removed."/>
80 </when>
81 <when value="names">
82 <param argument="name" type="data" format="mothur.names" label="name - Sequence names"/>
83 </when>
84 </conditional>
85 <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false"
86 label="dereplicate - remove chimeric sequences from all groups?"
87 help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/>
88 <param argument="minh" type="float" value="0.3" min="0" label="minh - mininum score to report chimera. Default 0.3"
89 help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/>
90 <param argument="mindiv" type="float" value="0.5" min="0" label="mindiv - minimum divergence ratio"
91 help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1. Default 0.5"/>
92 <param argument="xn" type="float" value="8.0" min="0" label="xn - weight of a no vote. Default 8.0"
93 help="Decreasing this weight to around 3 or 4 may give better performance on denoised data"/>
94 <param argument="dn" type="float" value="1.4" min="0" label="dn - pseudo-count prior on number of no votes"
95 help="Reasonable values are probably in the range from 0.2 to 2.0. Default 1.4"/>
96 <param argument="mindiffs" type="integer" value="3" min="0" label="minimum number of differences in segment"/>
97 <expand macro="param-savelog"/>
98 </inputs>
99 <outputs>
100 <expand macro="logfile-output"/>
101 <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/>
102 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/>
103 </outputs>
104 <tests>
105 <test><!-- de novo test with name file -->
106 <param name="fasta" value="stool_small.unique.fasta"/>
107 <param name="source" value="names"/>
108 <param name="name" value="stool_small.names"/>
109 <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
110 <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
111 <param name="savelog" value="true"/>
112 <expand macro="logfile-test"/>
113 </test>
114 <test><!-- de novo test with count table-->
115 <param name="fasta" value="stool_small.unique.fasta"/>
116 <param name="source" value="self"/>
117 <param name="count" value="stool_small.count_table"/>
118 <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
119 <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
120 <param name="savelog" value="true"/>
121 <expand macro="logfile-test"/>
122 </test>
123 <test><!-- test with reference file -->
124 <param name="fasta" value="stool_small.unique.fasta"/>
125 <param name="source" value="hist"/>
126 <param name="reference" value="stool_small.unique.fasta"/>
127 <output name="vsearch.chimeras" ftype="txt">
128 <assert_contents>
129 <expand macro="test-chimera-format"/>
130 <has_text text="F11Fcsw_12747"/>
131 </assert_contents>
132 </output>
133 <output name="out_accnos" ftype="mothur.accnos">
134 <assert_contents>
135 <expand macro="test-accnos-format"/>
136 <has_text text="F11Fcsw_23322"/>
137 </assert_contents>
138 </output>
139 <param name="savelog" value="true"/>
140 <expand macro="logfile-test"/>
141 </test>
142 </tests>
143 <help><![CDATA[
144
145 @MOTHUR_OVERVIEW@
146
147 **Command Documentation**
148
149 The chimera.vsearch_ command reads a fasta file and reference file and outputs potentially chimeric sequences.
150
151 .. _chimera.vsearch: https://www.mothur.org/wiki/Chimera.vsearch
152
153 ]]></help>
154 <expand macro="citations"/>
155 </tool>