Mercurial > repos > iuc > mothur_chimera_uchime

comparison chimera.uchime.xml @ 2:d1e70be881e5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:21:36 -0400
parents 6dc4f9beec9f
children 4e3780d096af
comparison
equal deleted inserted replaced
1:94ec0c5a826f 2:d1e70be881e5
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 #if $template.source == "self": 14 #if $template.source == "self":
15 ln -s "$template.count" template.count.dat && 15 ln -s '$template.count' template.count.dat &&
16 ln -s "$template.group" template.group.dat && 16 ln -s '$template.group' template.group.dat &&
17 #elif $template.source == "names": 17 #elif $template.source == "names":
18 ln -s "$template.name" template.name.dat && 18 ln -s '$template.name' template.name.dat &&
19 #else: 19 #else:
20 ln -s "$template.reference" template.reference.dat && 20 ln -s '$template.reference' template.reference.dat &&
21 #end if 21 #end if
22 22
23 echo 'chimera.uchime( 23 echo 'chimera.uchime(
24 fasta=fasta.dat, 24 fasta=fasta.dat,
25 #if $template.source == "self": 25 #if $template.source == "self":
26 reference=self, 26 reference=self,
27 #if float($template.abskew) > 0: 27 #if float($template.abskew) > 0:
28 abskew=$template.abskew, 28 abskew=$template.abskew,
29 #end if 29 #end if
30 #if $template.group: 30 #if $template.group:
31 group=template.group.dat, 31 group=template.group.dat,
32 #end if 32 #end if
33 #if $template.count: 33 #if $template.count:
34 count=template.count.dat, 34 count=template.count.dat,
35 #end if 35 #end if
36 #elif $template.source == "names": 36 #elif $template.source == "names":
37 name=template.name.dat, 37 name=template.name.dat,
38 #else: 38 #else:
39 reference=template.reference.dat, 39 reference=template.reference.dat,
40 #end if 40 #end if
41 minh=$minh, 41 minh=$minh,
42 mindiv=$mindiv, 42 mindiv=$mindiv,
43 xn=$xn, 43 xn=$xn,
44 dn=$dn, 44 dn=$dn,
45 xa=$xa, 45 xa=$xa,
46 chunks=$chunks, 46 chunks=$chunks,
47 minchunk=$minchunk, 47 minchunk=$minchunk,
48 #if $idsmoothwindow: 48 #if $idsmoothwindow:
49 idsmoothwindow=$idsmoothwindow, 49 idsmoothwindow=$idsmoothwindow,
50 #end if 50 #end if
51 maxp=$maxp, 51 maxp=$maxp,
52 minlen=$minlen, 52 minlen=$minlen,
53 maxlen=$maxlen, 53 maxlen=$maxlen,
54 skipgaps=$skipgaps, 54 skipgaps=$skipgaps,
55 skipgaps2=$skipgaps2, 55 skipgaps2=$skipgaps2,
56 #if $alignment.ucl == "local": 56 #if $alignment.ucl == "local":
57 ucl=true, 57 ucl=true,
58 #if $alignment.queryfract: 58 #if $alignment.queryfract:
59 queryfract=$alignment.queryfract, 59 queryfract=$alignment.queryfract,
60 #end if 60 #end if
61 #end if 61 #end if
62 dereplicate=$dereplicate, 62 dereplicate=$dereplicate,
63 chimealns=$chimealns, 63 chimealns=$chimealns,
64 processors='\${GALAXY_SLOTS:-8}' 64 processors='\${GALAXY_SLOTS:-8}'
65 )' 65 )'
66 | sed 's/ //g' ## mothur trips over whitespace 66 | sed 's/ //g' ## mothur trips over whitespace
67 | mothur 67 | mothur
68 | tee mothur.out.log 68 | tee mothur.out.log
69 2>&1 ## uchime component writes output to stderr 69 2>&1 ## uchime component writes output to stderr
70 ]]></command> 70 ]]></command>
71 <inputs> 71 <inputs>
72 <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Aligned Sequences"/> 72 <param argument="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Aligned Sequences"/>
73 <conditional name="template"> 73 <conditional name="template">
74 <param name="source" type="select" label="Select Reference Template from" help=""> 74 <param name="source" type="select" label="Select Reference Template from">
75 <option value="hist">History</option> 75 <option value="hist">History</option>
76 <option value="ref">Cached Reference</option> 76 <option value="ref">Cached Reference</option>
77 <option value="self">Self</option> 77 <option value="self">Self</option>
78 <option value="names">Use a names file</option> 78 <option value="names">Use a names file</option>
79 </param> 79 </param>
80 <when value="ref"> 80 <when value="ref">
81 <param name="reference" type="select" label="reference - Select an alignment database " help=""> 81 <param argument="reference" type="select" label="reference - Select an alignment database">
82 <options from_data_table="mothur_aligndb"> 82 <options from_data_table="mothur_aligndb"/>
83 </options>
84 </param> 83 </param>
85 </when> 84 </when>
86 <when value="hist"> 85 <when value="hist">
87 <param name="reference" type="data" format="fasta" label="reference - Reference to align with" help=""/> 86 <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
88 </when> 87 </when>
89 <when value="self"> 88 <when value="self">
90 <param name="abskew" type="float" value="1.9" label="abskew - Abundance skew (default 1.9)" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query)"/> 89 <param argument="abskew" type="float" value="1.9" label="abskew - Abundance skew"
91 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference" help="use the more abundant sequences from the same sample to check the query sequence"/> 90 help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query). Default 1.9"/>
92 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="Generated by count.seqs. When you use a count file with group info and dereplicate=T, mothur will create a *.pick.count_table file containing seqeunces after chimeras are removed."/> 91 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"
92 help="use the more abundant sequences from the same sample to check the query sequence"/>
93 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table"
94 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."/>
93 </when> 95 </when>
94 <when value="names"> 96 <when value="names">
95 <param name="name" type="data" format="mothur.names" label="name - Sequence names"/> 97 <param argument="name" type="data" format="mothur.names" label="name - Sequence names"/>
96 </when> 98 </when>
97 </conditional> 99 </conditional>
98 <param name="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups, default=f" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/> 100 <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false"
99 <param name="skipgaps" type="boolean" falsevalue="false" truevalue="true" checked="true" label="skipgaps - columns containing gaps do not count as diffs. Default=T" help="controls how gapped columns affect counting of diffs"/> 101 label="dereplicate - remove chimeric sequences from all groups?"
100 <param name="skipgaps2" type="boolean" falsevalue="false" truevalue="true" checked="true" label="skipgaps2 - column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default=T" help="controls how gapped columns affect counting of diffs"/> 102 help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/>
101 <param name="chimealns" type="boolean" falsevalue="false" truevalue="true" checked="false" label="chimealns - Produce a file containing multiple alignments of query sequences to parents in human readable format. " help="Alignments show columns with differences that support or contradict a chimeric model."/> 103 <param argument="skipgaps" type="boolean" falsevalue="false" truevalue="true" checked="true"
102 <param name="minh" type="float" value="0.3" min="0" label="minh - mininum score to report chimera. Default 0.3" help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/> 104 label="skipgaps - columns containing gaps do not count as diffs"
103 <param name="mindiv" type="float" value="0.5" min="0" label="mindiv - minimum divergence ratio, default 0.5" help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1"/> 105 help="controls how gapped columns affect counting of diffs"/>
104 <param name="xn" type="float" value="8.0" min="0" label="xn - weight of a no vote. Default 8.0" help="Decreasing this weight to around 3 or 4 may give better performance on denoised data"/> 106 <param argument="skipgaps2" type="boolean" falsevalue="false" truevalue="true" checked="true"
105 <param name="dn" type="float" value="1.4" min="0" label="dn - pseudo-count prior on number of no votes. Default 1.4" help="Reasonable values are probably in the range from 0.2 to 2.0"/> 107 label="skipgaps2 - column is immediately adjacent to a column containing a gap, it is not counted as a diff"
106 <param name="xa" type="float" value="1.0" min="0" label="xa - eight of an abstain vote. Default 1.0" help="Reasonable values might range from 0.1 to 2.0"/> 108 help="controls how gapped columns affect counting of diffs"/>
107 <param name="chunks" type="integer" value="4" min="0" label="chunks - number of chunks. Default 4." help="number of chunks to extract from the query sequence when searching for parents."/> 109 <param argument="chimealns" type="boolean" falsevalue="false" truevalue="true" checked="false"
108 <param name="minchunk" type="integer" value="64" min="0" label="minchunk - minimum length of a chunk. Default 64." help=""/> 110 label="chimealns - Produce a file containing multiple alignments of query sequences to parents in human readable format"
109 <param name="maxp" type="integer" value="2" min="0" label="maxp - maximum number of candidate parents to consider. Default 2" help="increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit"/> 111 help="Alignments show columns with differences that support or contradict a chimeric model."/>
110 <param name="minlen" type="integer" value="10" min="0" label="minlen - minimum unaligned sequence length. Default 10" help="Applies to both query and reference sequences."/> 112 <param argument="minh" type="float" value="0.3" min="0" label="minh - mininum score to report chimera. Default 0.3"
111 <param name="maxlen" type="integer" value="10000" min="0" label="maxlen - maximum unaligned sequence length. Defaults 10000" help="Applies to both query and reference sequences."/> 113 help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/>
112 <param name="idsmoothwindow" type="integer" value="32" min="0" optional="True" label="idsmoothwindow - the length of id smoothing window. Default 32" help=""/> 114 <param argument="mindiv" type="float" value="0.5" min="0" label="mindiv - minimum divergence ratio"
115 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"/>
116 <param argument="xn" type="float" value="8.0" min="0" label="xn - weight of a no vote. Default 8.0"
117 help="Decreasing this weight to around 3 or 4 may give better performance on denoised data"/>
118 <param argument="dn" type="float" value="1.4" min="0" label="dn - pseudo-count prior on number of no votes"
119 help="Reasonable values are probably in the range from 0.2 to 2.0. Default 1.4"/>
120 <param argument="xa" type="float" value="1.0" min="0" label="xa - eight of an abstain vote"
121 help="Reasonable values might range from 0.1 to 2.0. Default 1.0"/>
122 <param argument="chunks" type="integer" value="4" min="0" label="chunks - number of chunks"
123 help="number of chunks to extract from the query sequence when searching for parents. Default 4."/>
124 <param argument="minchunk" type="integer" value="64" min="0" label="minchunk - minimum length of a chunk" help="Default 64"/>
125 <param argument="maxp" type="integer" value="2" min="0" label="maxp - maximum number of candidate parents to consider"
126 help="increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit. Default 2"/>
127 <param argument="minlen" type="integer" value="10" min="0" label="minlen - minimum unaligned sequence length"
128 help="Applies to both query and reference sequences. Default 10"/>
129 <param argument="maxlen" type="integer" value="10000" min="0" label="maxlen - maximum unaligned sequence length"
130 help="Applies to both query and reference sequences. Default 10000"/>
131 <param argument="idsmoothwindow" type="integer" value="32" min="0" optional="True" label="idsmoothwindow - the length of id smoothing window"
132 help="Default 32"/>
113 <conditional name="alignment"> 133 <conditional name="alignment">
114 <param name="ucl" type="select" label="ucl - Use local-X alignments" help="global-X is the default"> 134 <param argument="ucl" type="select" label="ucl - Use local-X alignments" help="global-X is the default">
115 <option value="global" selected="true">global</option> 135 <option value="global" selected="true">global</option>
116 <option value="local">local</option> 136 <option value="local">local</option>
117 </param> 137 </param>
118 <when value="global"/> 138 <when value="global"/>
119 <when value="local"> 139 <when value="local">
120 <param name="queryfract" type="float" value="0.5" min="0" max="1" label="queryfract - minimum fraction of the query sequence that must be covered by a local-X alignment. Default 0.5." help=""/> 140 <param argument="queryfract" type="float" value="0.5" min="0" max="1"
141 label="queryfract - minimum fraction of the query sequence that must be covered by a local-X alignment" help="Default 0.5"/>
121 </when> 142 </when>
122 </conditional> 143 </conditional>
144 <expand macro="param-savelog"/>
123 </inputs> 145 </inputs>
124 <outputs> 146 <outputs>
125 <expand macro="logfile-output"/> 147 <expand macro="logfile-output"/>
126 <data name="out_file" format="txt" from_work_dir="fasta.*uchime.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/> 148 <data name="uchime.chimeras" format="txt" from_work_dir="fasta.*uchime.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/>
127 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*uchime.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/> 149 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*uchime.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/>
128 <data name="out_alns" format="txt" from_work_dir="fasta.*uchime.alns" label="${tool.name} on ${on_string}: uchime.alns"> 150 <data name="out_alns" format="txt" from_work_dir="fasta.*uchime.alns" label="${tool.name} on ${on_string}: uchime.alns">
129 <filter>chimealns</filter> 151 <filter>chimealns</filter>
130 </data> 152 </data>
131 <data name="out_count" format="mothur.count_table" from_work_dir="template.*uchime.pick.count_table" label="${tool.name} on ${on_string}: uchime.count_table"> 153 <data name="out_count" format="mothur.count_table" from_work_dir="template.*uchime.pick.count_table" label="${tool.name} on ${on_string}: uchime.count_table">
132 <filter>template['count']</filter> 154 <filter>template['source'] == 'self' and template['count']</filter>
133 </data> 155 </data>
134 </outputs> 156 </outputs>
135 <tests> 157 <tests>
136 <test><!-- default params test --> 158 <test><!-- default params test -->
137 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera"/> 159 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera"/>
138 <param name="source" value="hist"/> 160 <param name="source" value="hist"/>
139 <param name="reference" value="HMP_MOCK.v35.align"/> 161 <param name="reference" value="HMP_MOCK.v35.align"/>
140 <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/> 162 <output name="uchime.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/>
141 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos" ftype="mothur.accnos"/> 163 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos" ftype="mothur.accnos"/>
164 <param name="savelog" value="true"/>
142 <expand macro="logfile-test"/> 165 <expand macro="logfile-test"/>
143 </test> 166 </test>
144 <test><!-- de novo test --> 167 <test><!-- de novo test -->
145 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> 168 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
146 <param name="source" value="self"/> 169 <param name="source" value="self"/>
147 <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras" ftype="txt"/> 170 <output name="uchime.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras" ftype="txt"/>
148 <output name="out_accnos" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.accnos"/> 171 <output name="out_accnos" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.accnos"/>
172 <param name="savelog" value="true"/>
149 <expand macro="logfile-test"/> 173 <expand macro="logfile-test"/>
150 </test> 174 </test>
151 <test><!-- with chimealns output --> 175 <test><!-- with chimealns output -->
152 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera"/> 176 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera"/>
153 <param name="source" value="hist"/> 177 <param name="source" value="hist"/>
154 <param name="reference" value="HMP_MOCK.v35.align"/> 178 <param name="reference" value="HMP_MOCK.v35.align"/>
155 <param name="chimealns" value="true"/> 179 <param name="chimealns" value="true"/>
156 <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/> 180 <output name="uchime.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/>
157 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos" ftype="mothur.accnos"/> 181 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos" ftype="mothur.accnos"/>
158 <output name="out_alns" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns" ftype="txt"/> 182 <output name="out_alns" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns" ftype="txt"/>
183 <param name="savelog" value="true"/>
159 <expand macro="logfile-test"/> 184 <expand macro="logfile-test"/>
160 </test> 185 </test>
161 </tests> 186 </tests>
162 <help> 187 <help><![CDATA[
163 <![CDATA[
164 188
165 @MOTHUR_OVERVIEW@ 189 @MOTHUR_OVERVIEW@
166 190
167 **Command Documentation** 191 **Command Documentation**
168 192
169 The chimera.uchime_ command reads a fasta file and reference file and outputs potentially chimeric sequences. The original uchime program was written by Robert C. Edgar and donated to the public domain, http://drive5.com/uchime 193 The chimera.uchime_ command reads a fasta file and reference file and outputs potentially chimeric sequences. The original uchime program was written by Robert C. Edgar and donated to the public domain, http://drive5.com/uchime
170 194
171 .. _chimera.uchime: https://www.mothur.org/wiki/Chimera.uchime 195 .. _chimera.uchime: https://www.mothur.org/wiki/Chimera.uchime
172 196
173 Version 1.23.0: Upgrades tool dependency to mothur 1.33 and adds support for count (mothur 1.28) and dereplicate (mothur 1.29) options. 197 Version 1.23.0: Upgrades tool dependency to mothur 1.33 and adds support for count (mothur 1.28) and dereplicate (mothur 1.29) options.
174 ]]> 198
175 </help> 199 ]]></help>
176 <expand macro="citations"/> 200 <expand macro="citations"/>
177 </tool> 201 </tool>