Mercurial > repos > iuc > mothur_chimera_uchime
comparison chimera.uchime.xml @ 2:d1e70be881e5 draft
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> |