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comparison lotus2.xml @ 6:fc78d02657a9 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f"
author earlhaminst
date Sat, 05 Jun 2021 09:49:25 +0000
parents 7f33525b85d0
children 692832801d70
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5:7f33525b85d0 6:fc78d02657a9
1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy3" 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@">2.06</token> 4 <token name="@VERSION@">2.07</token>
5 <xml name="refDB_macro"> 5 <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">
6 <conditional name="refDB_cond"> 6 <conditional name="refDB_cond">
7 <param argument="-refDB" type="select" label="Taxonomy reference database"> 7 <param argument="-refDB" type="select" label="Taxonomy reference database">
8 <option value="cached">Use a built-in taxonomy database</option> 8 <option value="cached">Use a built-in taxonomy database</option>
9 <option value="history">Use a taxonomy from history</option> 9 <option value="history">Use a taxonomy from history</option>
10 </param> 10 </param>
11 <when value="cached"> 11 <when value="cached">
12 <param argument="ref_db" type="select" label="Using reference database" help="Select database from the list"> 12 <param argument="-ref_db" type="select" label="Using reference database" help="Select database from the list">
13 <option value="SLV" selected="true">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option> 13 <option value="" selected="true">(Default)</option>
14 <option value="SLV">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option>
14 <option value="GG">Greengenes (GG)</option> 15 <option value="GG">Greengenes (GG)</option>
15 <option value="UNITE">ITS focused on fungi (UNITE)</option> 16 <option value="UNITE">ITS focused on fungi (UNITE)</option>
16 <option value="PR2">SSU focused on Protists (PR2)</option> 17 <option value="PR2">SSU focused on Protists (PR2)</option>
17 <option value="beetax">Bee gut specific database and tax names (beetax)</option> 18 <option value="beetax">Bee gut specific database and tax names (beetax)</option>
18 <option value="HITdb">Human gut microbiota (HITdb)</option> 19 <option value="HITdb">Human gut microbiota (HITdb)</option>
19 </param> 20 </param>
20 <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" /> 21 <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" />
21 </when> 22 </when>
22 <when value="history"> 23 <when value="history">
23 <param name="ref_fasta" type="data" format="fasta" label="Taxonomy reference sequences" help="In FASTA format" /> 24 <param name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" label="Taxonomy reference sequences" help="In FASTA format" />
24 <param argument="-tax4refDB" type="data" format="tabular" label="Taxonomy reference lineages" help="Tab-separated file with 2 columns mapping each FASTA header of the reference sequences to a GTDB-style taxonomy string" /> 25 <param argument="-tax4refDB" type="data" format="tabular" label="Taxonomy reference lineages" help="Tab-separated file with 2 columns mapping each FASTA header of the reference sequences to a GTDB-style taxonomy string" />
25 </when> 26 </when>
26 </conditional> 27 </conditional>
27 <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use the best Blast hit only" help="Do not use LCA (lowest common ancestor) to determine the most likely taxonomic level (not recommended)" /> 28 <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use the best Blast hit only" help="Do not use LCA (lowest common ancestor) to determine the most likely taxonomic level (not recommended)" />
28 </xml> 29 </xml>
29 <xml name="id_macro"> 30 <xml name="id_macro">
30 <param argument="-id" type="float" min="0" max="1" value="0.97" label="Clustering threshold for OTUs" /> 31 <param argument="-id" type="float" min="0.9" max="1" value="" optional="true" label="Clustering threshold for OTUs" />
31 </xml> 32 </xml>
32 <xml name="ITSx_macro"> 33 <xml name="ITSx_macro">
33 <param argument="-ITSx" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use ITSx to only retain OTUs fitting to ITS1/ITS2 hmm models" /> 34 <param argument="-ITSx" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use ITSx to only retain OTUs fitting to ITS1/ITS2 hmm models" />
34 </xml> 35 </xml>
35 </macros> 36 </macros>
39 <version_command>lotus2 --version</version_command> 40 <version_command>lotus2 --version</version_command>
40 <command detect_errors="exit_code"><![CDATA[ 41 <command detect_errors="exit_code"><![CDATA[
41 #import os.path 42 #import os.path
42 #import re 43 #import re
43 #def symlink_basename($f): 44 #def symlink_basename($f):
44 #set fn = re.sub('[^\w\-_.]', '_', $f.element_identifier) 45 #set $fn = re.sub('[^\w\-_.]', '_', $f.element_identifier)
45 #if fn.endswith('.gz'): 46 #if $fn.endswith('.gz'):
46 #set fn = fn[:-3] 47 #set $fn = $fn[:-3]
47 #end if 48 #end if
48 #for ext in ('.fq', '.fastq', '.fastqsanger'): 49 #if $f.ext.startswith('fastqsanger'):
49 #if fn.endswith($ext): 50 #set $exts_to_drop = ('.fq', '.fastq', '.fastqsanger')
50 #set fn = fn[:-len($ext)] 51 #elif $f.ext.startswith('fasta'):
52 #set $exts_to_drop = ('.fa', '.fasta', '.fna')
53 #else
54 #set $exts_to_drop = []
55 #end if
56 #for $ext in $exts_to_drop:
57 #if $fn.endswith($ext):
58 #set $fn = $fn[:-len($ext)]
51 #break 59 #break
52 #end if 60 #end if
53 #end for 61 #end for
54 $fn#slurp 62 $fn#slurp
55 #end def 63 #end def
56 64
57 mkdir input 65 mkdir input
58 && 66 &&
59 #if $inputs.paired_or_single == 'single': 67 #if $inputs.paired_or_single == 'single':
60 #for f in $inputs.input: 68 #for $f in $inputs.input:
61 #set ext = $f.ext.replace('sanger', '') 69 #set $ext = $f.ext.replace('sanger', '')
62 ln -s '$f' 'input/${symlink_basename(f)}.${ext}' && 70 ln -s '$f' 'input/${symlink_basename(f)}.${ext}' &&
63 #end for 71 #end for
64 #elif $inputs.paired_or_single == 'paired': 72 #elif $inputs.paired_or_single == 'paired':
65 #for i, f in enumerate($inputs.left_input): 73 #for i, f in enumerate($inputs.left_input):
66 #set ext = $f.ext.replace('sanger', '') 74 #set ext = $f.ext.replace('sanger', '')
67 ln -s '$f' 'input/input${i}.1.${ext}' && 75 ln -s '$f' 'input/input${i}.1.${ext}' &&
68 #end for 76 #end for
69 #for i, f in enumerate($inputs.right_input): 77 #for $i, $f in enumerate($inputs.right_input):
70 #set ext = $f.ext.replace('sanger', '') 78 #set $ext = $f.ext.replace('sanger', '')
71 ln -s '$f' 'input/input${i}.2.${ext}' && 79 ln -s '$f' 'input/input${i}.2.${ext}' &&
72 #end for 80 #end for
73 #else: 81 #else:
74 #for f in $inputs.pair_input: 82 #for $f in $inputs.pair_input:
75 #set ext = $f.forward.ext.replace('sanger', '') 83 #set $ext = $f.forward.ext.replace('sanger', '')
76 ln -s '$f.forward' 'input/${symlink_basename(f)}.1.${ext}' && 84 ln -s '$f.forward' 'input/${symlink_basename(f)}.1.${ext}' &&
77 #set ext = $f.reverse.ext.replace('sanger', '') 85 #set $ext = $f.reverse.ext.replace('sanger', '')
78 ln -s '$f.reverse' 'input/${symlink_basename(f)}.2.${ext}' && 86 ln -s '$f.reverse' 'input/${symlink_basename(f)}.2.${ext}' &&
79 #end for 87 #end for
88 #end if
89
90 #if $tax_args.aligner_cond.taxAligner not in ('0', '3') and $tax_args.aligner_cond.refDB_cond.refDB == 'history':
91 #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta) + '.' + $tax_args.aligner_cond.refDB_cond.ref_fasta.ext
92 ln -s '$tax_args.aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' &&
80 #end if 93 #end if
81 94
82 #if not $map: 95 #if not $map:
83 lotus2 -create_map mapping.txt -i input/ && 96 lotus2 -create_map mapping.txt -i input/ &&
84 cat mapping.txt && 97 cat mapping.txt &&
89 -i input/ 102 -i input/
90 -o output 103 -o output
91 -tmpDir tmp_folder 104 -tmpDir tmp_folder
92 -threads "\${GALAXY_SLOTS:-1}" 105 -threads "\${GALAXY_SLOTS:-1}"
93 -map '$map' 106 -map '$map'
94 -platform $platform 107 #if $sdmopt:
108 -sdmopt '$sdmopt'
109 #end if
110 #if $platform != '':
111 -platform $platform
112 #end if
95 #if $barcode: 113 #if $barcode:
96 -barcode '$barcode' 114 -barcode '$barcode'
97 #end if 115 #end if
98 #if $forwardPrimer: 116 #if $forwardPrimer:
99 -forwardPrimer '$forwardPrimer' 117 -forwardPrimer '$forwardPrimer'
104 #if $offtarget_cond.offtargetDB != 'no': 122 #if $offtarget_cond.offtargetDB != 'no':
105 -offtargetDB '$offtarget_cond.ref_file' 123 -offtargetDB '$offtarget_cond.ref_file'
106 #end if 124 #end if
107 125
108 -clustering $clu_args.clu_cond.clustering 126 -clustering $clu_args.clu_cond.clustering
109 #if $clu_args.clu_cond.clustering in ('1', '3'): 127 #if $clu_args.clu_cond.clustering in ('1', '3') and str($clu_args.clu_cond.id):
110 -id $clu_args.clu_cond.id 128 -id $clu_args.clu_cond.id
111 #elif $clu_args.clu_cond.clustering == '2': 129 #elif $clu_args.clu_cond.clustering == '2':
112 -swarm_distance $clu_args.clu_cond.swarm_distance 130 -swarm_distance $clu_args.clu_cond.swarm_distance
113 #end if 131 #end if
114 #if $clu_args.derepMin: 132 #if $clu_args.derepMin:
115 -derepMin '$clu_args.derepMin' 133 -derepMin '$clu_args.derepMin'
116 #end if 134 #end if
117 -deactivateChimeraCheck $clu_args.deactivateChimeraCheck 135
118 -chim_skew $clu_args.chim_skew 136 #if $clu_args.deactivateChimeraCheck != '':
137 -deactivateChimeraCheck $clu_args.deactivateChimeraCheck
138 #end if
139 #if str($clu_args.chim_skew):
140 -chim_skew $clu_args.chim_skew
141 #end if
119 142
120 -taxAligner $tax_args.aligner_cond.taxAligner 143 -taxAligner $tax_args.aligner_cond.taxAligner
121 #if $tax_args.aligner_cond.taxAligner == '0': 144 #if $tax_args.aligner_cond.taxAligner == '0':
122 -rdp_thr $tax_args.aligner_cond.rdp_thr 145 -rdp_thr $tax_args.aligner_cond.rdp_thr
123 #elif $tax_args.aligner_cond.taxAligner == '3': 146 #elif $tax_args.aligner_cond.taxAligner == '3':
124 -utax_thr $tax_args.aligner_cond.utax_thr 147 -utax_thr $tax_args.aligner_cond.utax_thr
125 #else: 148 #else:
126 #if $tax_args.aligner_cond.refDB_cond.refDB == 'cached': 149 #if $tax_args.aligner_cond.refDB_cond.refDB == 'cached':
127 -refDB $tax_args.aligner_cond.refDB_cond.ref_db 150 #if $tax_args.aligner_cond.refDB_cond.ref_db != '':
128 -greengenesSpecies $tax_args.aligner_cond.refDB_cond.greengenesSpecies 151 -refDB $tax_args.aligner_cond.refDB_cond.ref_db
152 -greengenesSpecies $tax_args.aligner_cond.refDB_cond.greengenesSpecies
153 #end if
129 #else: 154 #else:
130 -refDB $tax_args.aligner_cond.refDB_cond.ref_fasta 155 -refDB '$ref_fasta_symlink'
131 -tax4refDB $tax_args.aligner_cond.refDB_cond.tax4refDB 156 -tax4refDB '$tax_args.aligner_cond.refDB_cond.tax4refDB'
132 #end if 157 #end if
133 -useBestBlastHitOnly $tax_args.aligner_cond.useBestBlastHitOnly 158 -useBestBlastHitOnly $tax_args.aligner_cond.useBestBlastHitOnly
134 #end if 159 #end if
135 -amplicon_type $tax_args.amplicon_cond.amplicon_type 160 #if $tax_args.amplicon_cond.amplicon_type != '':
161 -amplicon_type $tax_args.amplicon_cond.amplicon_type
162 #end if
136 #if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'): 163 #if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'):
137 -ITSx $tax_args.amplicon_cond.ITSx_macro 164 -ITSx $tax_args.amplicon_cond.ITSx_macro
138 #end if 165 #end if
139 -tax_group $tax_args.tax_group 166
167 #if $tax_args.tax_group != '':
168 -tax_group $tax_args.tax_group
169 #end if
140 -keepUnclassified $tax_args.keepUnclassified 170 -keepUnclassified $tax_args.keepUnclassified
141 -LCA_cover $tax_args.LCA_cover 171 #if str($tax_args.LCA_cover):
142 -LCA_frac $tax_args.LCA_frac 172 -LCA_cover $tax_args.LCA_cover
173 #end if
174 #if str($tax_args.LCA_frac):
175 -LCA_frac $tax_args.LCA_frac
176 #end if
143 -lulu $tax_args.lulu 177 -lulu $tax_args.lulu
144 -buildPhylo $tax_args.buildPhylo 178 -buildPhylo $tax_args.buildPhylo
145 179
146 ; EXIT_VALUE=\$? ; 180 ; EXIT_VALUE=\$? ;
147 181
168 <when value="paired_collection"> 202 <when value="paired_collection">
169 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="List of paired reads" /> 203 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="List of paired reads" />
170 </when> 204 </when>
171 </conditional> 205 </conditional>
172 <param argument="-map" type="data" format="tabular" optional="true" label="Mapping file (optional)" help="Needed to demultiplex the FASTQ files using sdm. If the FASTQ are already demultiplexed, this can be omitted." /> 206 <param argument="-map" type="data" format="tabular" optional="true" label="Mapping file (optional)" help="Needed to demultiplex the FASTQ files using sdm. If the FASTQ are already demultiplexed, this can be omitted." />
207 <param argument="-sdmopt" type="data" format="txt" optional="true" label="SDM option file (optional)" />
173 <param argument="-platform" type="select" label="Sequencing platform"> 208 <param argument="-platform" type="select" label="Sequencing platform">
174 <option value="miSeq" selected="true">miSeq</option> 209 <option value="" selected="true">(Default)</option>
210 <option value="miSeq">miSeq</option>
175 <option value="hiSeq">hiSeq</option> 211 <option value="hiSeq">hiSeq</option>
176 <option value="454">454</option> 212 <option value="454">454</option>
177 <option value="PacBio">PacBio</option> 213 <option value="PacBio">PacBio</option>
178 </param> 214 </param>
179 <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" /> 215 <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" />
193 <validator type="no_options" message="No reference genomes are available" /> 229 <validator type="no_options" message="No reference genomes are available" />
194 </options> 230 </options>
195 </param> 231 </param>
196 </when> 232 </when>
197 <when value="history"> 233 <when value="history">
198 <param name="ref_file" type="data" format="fasta" label="FASTA reference genome" /> 234 <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
199 </when> 235 </when>
200 </conditional> 236 </conditional>
201 <section name="clu_args" title="Clustering Options"> 237 <section name="clu_args" title="Clustering Options">
202 <conditional name="clu_cond"> 238 <conditional name="clu_cond">
203 <param argument="-clustering" type="select" label="Clustering algorithm"> 239 <param argument="-clustering" type="select" label="Clustering algorithm">
221 <when value="7"> 257 <when value="7">
222 </when> 258 </when>
223 </conditional> 259 </conditional>
224 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" 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. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." /> 260 <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" 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. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." />
225 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check"> 261 <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">
226 <option value="0" selected="true">OTU chimera checks</option> 262 <option value="" selected="true">(Default)</option>
263 <option value="0">OTU chimera checks</option>
227 <option value="1">No chimera check at all</option> 264 <option value="1">No chimera check at all</option>
228 <option value="2">Disable deNovo chimera check</option> 265 <option value="2">Disable deNovo chimera check</option>
229 <option value="3">Disable ref based chimera check</option> 266 <option value="3">Disable ref based chimera check</option>
230 </param> 267 </param>
231 <param argument="-chim_skew" type="integer" min="0" value="2" label="Skew in chimeric fragment abundance" /> 268 <param argument="-chim_skew" type="integer" min="0" value="" optional="true" label="Skew in chimeric fragment abundance" />
232 </section> 269 </section>
233 <section name="tax_args" title="Taxonomy Options"> 270 <section name="tax_args" title="Taxonomy Options">
234 <conditional name="aligner_cond"> 271 <conditional name="aligner_cond">
235 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs"> 272 <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs">
236 <option value="0" selected="true">RDPclassifier (max likelihood)</option> 273 <option value="0" selected="true">RDPclassifier (max likelihood)</option>
241 </param> 278 </param>
242 <when value="0"> 279 <when value="0">
243 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/> 280 <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/>
244 </when> 281 </when>
245 <when value="1"> 282 <when value="1">
246 <expand macro="refDB_macro" /> 283 <expand macro="refDB_macro" ref_fasta_formats="fasta" />
247 </when> 284 </when>
248 <when value="2"> 285 <when value="2">
249 <expand macro="refDB_macro" /> 286 <expand macro="refDB_macro" />
250 </when> 287 </when>
251 <when value="3"> 288 <when value="3">
255 <expand macro="refDB_macro" /> 292 <expand macro="refDB_macro" />
256 </when> 293 </when>
257 </conditional> 294 </conditional>
258 <conditional name="amplicon_cond"> 295 <conditional name="amplicon_cond">
259 <param argument="-amplicon_type" type="select" label="Amplicon type"> 296 <param argument="-amplicon_type" type="select" label="Amplicon type">
297 <option value="" selected="true">(Default)</option>
260 <option value="LSU">LSU Large subunit (23S/28S)</option> 298 <option value="LSU">LSU Large subunit (23S/28S)</option>
261 <option value="SSU" selected="true">SSU small subunit (16S/18S)</option> 299 <option value="SSU">SSU small subunit (16S/18S)</option>
262 <option value="ITS">ITS internal transcribed spacer</option> 300 <option value="ITS">ITS internal transcribed spacer</option>
263 <option value="ITS1">ITS1</option> 301 <option value="ITS1">ITS1</option>
264 <option value="ITS2">ITS2</option> 302 <option value="ITS2">ITS2</option>
265 </param> 303 </param>
266 <when value="ITS"> 304 <when value="ITS">
272 <when value="ITS2"> 310 <when value="ITS2">
273 <expand macro="ITSx_macro" /> 311 <expand macro="ITSx_macro" />
274 </when> 312 </when>
275 </conditional> 313 </conditional>
276 <param argument="-tax_group" type="select" label="Tax group"> 314 <param argument="-tax_group" type="select" label="Tax group">
277 <option value="bacteria" selected="true">bacterial 16S rDNA annnotation</option> 315 <option value="" selected="true">(Default)</option>
316 <option value="bacteria">bacterial 16S rDNA annnotation</option>
278 <option value="fungi">fungal 18S/23S/ITS annotation</option> 317 <option value="fungi">fungal 18S/23S/ITS annotation</option>
279 </param> 318 </param>
280 <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" /> 319 <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" />
281 <param argument="-LCA_cover" type="float" min="0" max="1" value="0.9" label="Minimum horizontal coverage of an OTU sequence against ref DB"/> 320 <param argument="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB"/>
282 <param argument="-LCA_frac" type="float" min="0" max="1" value="0.9" label="Minimum fraction of reads with identical taxonomy"/> 321 <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy"/>
283 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" /> 322 <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" />
284 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny"> 323 <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
285 <option value="0">Disable</option> 324 <option value="0">Disable</option>
286 <option value="1" selected="true">Use fasttree2</option> 325 <option value="1" selected="true">Use fasttree2</option>
287 <option value="2">Use iqtree2</option> 326 <option value="2">Use iqtree2</option>