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comparison lotus2.xml @ 1:85da3173a488 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
author earlhaminst
date Wed, 19 May 2021 02:38:24 +0000
parents 478e767a0e7a
children cf56a6553385
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0:478e767a0e7a 1:85da3173a488
1 <tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01"> 1 <tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01">
2 <description>fast OTU processing pipeline</description> 2 <description>fast OTU processing pipeline</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">2.04</token> 4 <token name="@VERSION@">2.05.1</token>
5 <xml name="refDB_macro">
6 <param argument="-refDB" type="select" label="Reference Database">
7 <option value="SLV" selected="true">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option>
8 <option value="GG">Greengenes (GG)</option>
9 <option value="UNITE">ITS focused on fungi (UNITE)</option>
10 <option value="PR2">SSU focused on Protists (PR2)</option>
11 <option value="beetax">Bee gut specific database and tax names (beetax)</option>
12 <option value="HITdb">Human gut microbiota (HITdb)</option>
13 </param>
14 </xml>
5 </macros> 15 </macros>
6 <requirements> 16 <requirements>
7 <requirement type="package" version="@VERSION@">lotus2</requirement> 17 <requirement type="package" version="@VERSION@">lotus2</requirement>
8 </requirements> 18 </requirements>
9 <version_command>lotus2 --version</version_command> 19 <version_command>lotus2 --version</version_command>
53 -reversePrimer '$reversePrimer' 63 -reversePrimer '$reversePrimer'
54 #end if 64 #end if
55 65
56 -clustering $clu_args.clustering 66 -clustering $clu_args.clustering
57 -id $clu_args.id 67 -id $clu_args.id
58 -derepMin $clu_args.derepMin 68 #if $clu_args.derepMin:
69 -derepMin '$clu_args.derepMin'
70 #end if
71 -deactivateChimeraCheck $clu_args.deactivateChimeraCheck
59 -chim_skew $clu_args.chim_skew 72 -chim_skew $clu_args.chim_skew
60 -deactivateChimeraCheck $clu_args.deactivateChimeraCheck
61 -readOverlap $clu_args.readOverlap 73 -readOverlap $clu_args.readOverlap
62 74
63 -refDB $tax_args.refDB 75 -taxAligner $tax_args.aligner_cond.taxAligner
76 #if $tax_args.aligner_cond.taxAligner == '0':
77 -rdp_thr $tax_args.aligner_cond.rdp_thr
78 #elif $tax_args.aligner_cond.taxAligner == '3':
79 -utax_thr $tax_args.aligner_cond.utax_thr
80 #else:
81 -refDB $tax_args.aligner_cond.refDB
82 #end if
64 -amplicon_type $tax_args.amplicon_type 83 -amplicon_type $tax_args.amplicon_type
65 -tax_group $tax_args.tax_group 84 -tax_group $tax_args.tax_group
66 -rdp_thr $tax_args.rdp_thr
67 -utax_thr $tax_args.utax_thr
68 -keepUnclassified $tax_args.keepUnclassified 85 -keepUnclassified $tax_args.keepUnclassified
69 -taxAligner $tax_args.taxAligner
70 -useBestBlastHitOnly $tax_args.useBestBlastHitOnly 86 -useBestBlastHitOnly $tax_args.useBestBlastHitOnly
71 -LCA_cover $tax_args.LCA_cover 87 -LCA_cover $tax_args.LCA_cover
72 -LCA_frac $tax_args.LCA_frac 88 -LCA_frac $tax_args.LCA_frac
73 -greengenesSpecies $tax_args.greengenesSpecies 89 -greengenesSpecies $tax_args.greengenesSpecies
74 -pseudoRefOTUcalling $tax_args.pseudoRefOTUcalling 90
75 91 ; EXIT_VALUE=\$? ;
92
93 tar -cvzf output.tar.gz output/
76 && 94 &&
77 95 exit \$EXIT_VALUE
78 cd output/ &&
79 tar -cvzf higherLvl.tar.gz higherLvl/ &&
80 tar -cvzf ExtraFiles.tar.gz ExtraFiles/ &&
81 tar -cvzf LotuSLogS.tar.gz LotuSLogS/ &&
82 tar -cvzf primary.tar.gz primary/
83 ]]></command> 96 ]]></command>
84 97
85 <inputs> 98 <inputs>
86 <conditional name="inputs"> 99 <conditional name="inputs">
87 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 100 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
104 <option value="miSeq" selected="true">miSeq</option> 117 <option value="miSeq" selected="true">miSeq</option>
105 <option value="hiSeq">hiSeq</option> 118 <option value="hiSeq">hiSeq</option>
106 <option value="454">454</option> 119 <option value="454">454</option>
107 <option value="PacBio">PacBio</option> 120 <option value="PacBio">PacBio</option>
108 </param> 121 </param>
109 <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcodes (MIDs)" help="FASTQ file with barcodes (in the processed mi/hiSeq format)" /> 122 <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcode (MID) sequences (optional)" help="FASTQ file with barcodes (in the processed mi/hiSeq format), if provided by the sequencer" />
110 <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region" help="E.g. 16S primer fwd" /> 123 <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region" help="E.g. 16S primer fwd" />
111 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region" help="E.g. 16S primer rev" /> 124 <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region" help="E.g. 16S primer rev" />
112 <section name="clu_args" title="Clustering Options"> 125 <section name="clu_args" title="Clustering Options">
113 <param argument="-clustering" type="select" label="Clustering algorithm"> 126 <param argument="-clustering" type="select" label="Clustering algorithm">
114 <option value="1">UPARSE</option> 127 <option value="1">UPARSE</option>
115 <option value="2">swarm</option> 128 <option value="2">swarm</option>
116 <option value="3" selected="true">cd-hit</option> 129 <option value="3">cd-hit</option>
117 <option value="6">unoise3</option> 130 <option value="6">unoise3</option>
118 <option value="7">dada2</option> 131 <option value="7" selected="true">dada2</option>
119 </param> 132 </param>
120 <param argument="-id" type="float" min="0" max="1" value="0.97" label="Clustering threshold for OTUs" /> 133 <param argument="-id" type="float" min="0" max="1" value="0.97" label="Clustering threshold for OTUs" />
121 <param argument="-derepMin" type="integer" min="0" value="1" label="Minimum size of dereplicated clustered" /> 134 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads" help="E.g. 4:1,4:2,3:3 . See http://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter" />
122 <param argument="-chim_skew" type="integer" min="0" value="2" label="Skew in chimeric fragment abundance" />
123 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check"> 135 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">
124 <option value="0" selected="true">OTU chimera checks</option> 136 <option value="0" selected="true">OTU chimera checks</option>
125 <option value="1">No chimera check at all</option> 137 <option value="1">No chimera check at all</option>
126 <option value="2">Deactivate deNovo chimera check</option> 138 <option value="2">Deactivate deNovo chimera check</option>
127 <option value="3">Deactivate ref based chimera check</option> 139 <option value="3">Deactivate ref based chimera check</option>
128 </param> 140 </param>
141 <param argument="-chim_skew" type="integer" min="0" value="2" label="Skew in chimeric fragment abundance" />
129 <param argument="-readOverlap" type="integer" min="0" value="300" label="Maximum number of basepairs that two reads are overlapping" /> 142 <param argument="-readOverlap" type="integer" min="0" value="300" label="Maximum number of basepairs that two reads are overlapping" />
130 </section> 143 </section>
131 <section name="tax_args" title="Taxonomy Options"> 144 <section name="tax_args" title="Taxonomy Options">
132 <param argument="-refDB" type="select" label="Reference Database"> 145 <conditional name="aligner_cond">
133 <option value="SLV" selected="true">Silva LSU (23/28S) or SSU (16/18S)</option> 146 <param argument="-taxAligner" type="select" label="Taxonomy aligner">
134 <option value="GG">Greengenes</option> 147 <option value="0" selected="true">Deactivated (just use RDP)</option>
135 <option value="UNITE">ITS focused on fungi</option> 148 <option value="1">Blast</option>
136 <option value="PR2">SSU focused on Protists</option> 149 <option value="2">Use LAMBDA to search against a 16S reference database for taxonomic profiling of OTUs</option>
137 <option value="beetax">Bee gut specific database and tax names</option> 150 <option value="3">Use UTAX with custom databases</option>
138 <option value="HITdb">Human gut microbiota</option> 151 <option value="4">Use VSEARCH to align OTUs to custom databases</option>
139 </param> 152 </param>
153 <when value="0">
154 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/>
155 </when>
156 <when value="1">
157 <expand macro="refDB_macro" />
158 </when>
159 <when value="2">
160 <expand macro="refDB_macro" />
161 </when>
162 <when value="3">
163 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for UTAX"/>
164 </when>
165 <when value="4">
166 <expand macro="refDB_macro" />
167 </when>
168 </conditional>
140 <param argument="-amplicon_type" type="select" label="Amplicon type"> 169 <param argument="-amplicon_type" type="select" label="Amplicon type">
141 <option value="LSU">LSU Large subunit (23S/28S)</option> 170 <option value="LSU">LSU Large subunit (23S/28S)</option>
142 <option value="SSU" selected="true">SSU small subunit (16S/18S)</option> 171 <option value="SSU" selected="true">SSU small subunit (16S/18S)</option>
143 <option value="ITS">ITS internal transcribed spacer</option> 172 <option value="ITS">ITS internal transcribed spacer</option>
144 <option value="ITS1">ITS1</option> 173 <option value="ITS1">ITS1</option>
146 </param> 175 </param>
147 <param argument="-tax_group" type="select" label="Tax group"> 176 <param argument="-tax_group" type="select" label="Tax group">
148 <option value="bacteria" selected="true">bacterial 16S rDNA annnotation</option> 177 <option value="bacteria" selected="true">bacterial 16S rDNA annnotation</option>
149 <option value="fungi">fungal 18S/23S/ITS annotation</option> 178 <option value="fungi">fungal 18S/23S/ITS annotation</option>
150 </param> 179 </param>
151 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/>
152 <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for UTAX"/>
153 <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (i.e. no match in RDP/Blast database) in OTU and taxa abundance matrix calculations" /> 180 <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (i.e. no match in RDP/Blast database) in OTU and taxa abundance matrix calculations" />
154 <param argument="-taxAligner" type="select" label="Taxonomy aligner">
155 <option value="0" selected="true">Deactivated (just use RDP)</option>
156 <option value="1">Blast</option>
157 <option value="2">Use LAMBDA to search against a 16S reference database for taxonomic profiling of OTUs</option>
158 <option value="3">Use UTAX with custom databases</option>
159 <option value="4">Use VSEARCH to align OTUs to custom databases</option>
160 <option value="5">Use USEARCH to align OTUs to custom databases</option>
161 </param>
162 <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use best blast hit only" help="If selected, do not use LCA (lowest common ancestor) to determine most likely taxonomic level (not recommended)" /> 181 <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use best blast hit only" help="If selected, do not use LCA (lowest common ancestor) to determine most likely taxonomic level (not recommended)" />
163 <param argument="-LCA_cover" type="float" min="0" max="1" value="0.9" label="Minimum horizontal coverage of an OTU sequence against ref DB"/> 182 <param argument="-LCA_cover" type="float" min="0" max="1" value="0.9" label="Minimum horizontal coverage of an OTU sequence against ref DB"/>
164 <param argument="-LCA_frac" type="float" min="0" max="1" value="0.9" label="Minimum fraction of reads with identical taxonomy"/> 183 <param argument="-LCA_frac" type="float" min="0" max="1" value="0.9" label="Minimum fraction of reads with identical taxonomy"/>
165 <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" /> 184 <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" />
166 <param argument="-pseudoRefOTUcalling" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create Reference based (open) OTUs" />
167 </section> 185 </section>
168 </inputs> 186 </inputs>
169 187
170 <outputs> 188 <outputs>
171 <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" /> 189 <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />
172 <data name="otu_biom" format="biom" label="${tool.name} on ${on_string}: biom-formatted OTU abundance matrix" from_work_dir="output/OTU.biom" /> 190 <data name="otu_biom" format="biom" label="${tool.name} on ${on_string}: biom-formatted OTU abundance matrix" from_work_dir="output/OTU.biom" />
173 <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" /> 191 <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />
174 <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" /> 192 <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />
175 <data name="hiera_blast" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on Blastn" from_work_dir="output/hiera_BLAST.txt" /> 193 <data name="hiera_blast" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on Blastn" from_work_dir="output/hiera_BLAST.txt" />
176 <data name="hiera_rdp" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on RDP classifier" from_work_dir="output/hiera_RDP.txt" /> 194 <data name="hiera_rdp" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on RDP classifier" from_work_dir="output/hiera_RDP.txt" />
177 <data name="primary" format="tar" label="${tool.name} on ${on_string}: Copies of sdm options and mapping file" from_work_dir="output/primary.tar.gz" /> 195 <data name="primary" format="tar" label="${tool.name} on ${on_string}: All output files" from_work_dir="output.tar.gz" />
178 <data name="higherlvl" format="tar" label="${tool.name} on ${on_string}: Abundance matrices" from_work_dir="output/higherLvl.tar.gz" />
179 <data name="lotuslogs" format="tar" label="${tool.name} on ${on_string}: Log files" from_work_dir="output/LotuSLogS.tar.gz" />
180 <data name="extrafiles" format="tar" label="${tool.name} on ${on_string}: Extra files" from_work_dir="output/ExtraFiles.tar.gz" />
181 </outputs> 196 </outputs>
182 197
183 <tests> 198 <tests>
184 <test> 199 <test>
185 <param name="paired_or_single" value="single"/> 200 <param name="paired_or_single" value="single"/>
186 <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/> 201 <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>
187 <param name="platform" value="454" /> 202 <param name="platform" value="454" />
203 <param name="clustering" value="3" />
188 <output name="otu" file="OTU.txt" compare="sim_size" /> 204 <output name="otu" file="OTU.txt" compare="sim_size" />
189 <output name="otu_fna" file="OTU.fna" compare="sim_size" /> 205 <output name="otu_fna" file="OTU.fna" compare="sim_size" />
190 <output name="hiera_rdp" file="hiera_RDP.txt" compare="sim_size" /> 206 <output name="hiera_rdp" file="hiera_RDP.txt" compare="sim_size" />
191 </test> 207 </test>
192 </tests> 208 </tests>
195 If you have separate FASTA and quality files, these can be combined in a FASTQ file using the "Combine FASTA and QUAL into FASTQ" tool. 211 If you have separate FASTA and quality files, these can be combined in a FASTQ file using the "Combine FASTA and QUAL into FASTQ" tool.
196 212
197 Documentation can be found at `<http://lotus2.earlham.ac.uk/>`_. 213 Documentation can be found at `<http://lotus2.earlham.ac.uk/>`_.
198 ]]></help> 214 ]]></help>
199 <citations> 215 <citations>
200 <citation type="doi">10.1186/2049-2618-2-30</citation> 216 <citation type="doi">10.1186/s40168-021-01012-1</citation>
201 </citations> 217 </citations>
202 </tool> 218 </tool>