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comparison macros.xml @ 3:cc7863bec4e0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
author iuc
date Wed, 26 Jul 2023 07:34:34 +0000
parents 8b2b19eefc52
children 92a66ccb7e6c
comparison
equal deleted inserted replaced
2:ae86751e6f6d 3:cc7863bec4e0
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.6.1</token>
3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@PROFILE@">22.01</token>
2 <xml name="requirements"> 5 <xml name="requirements">
3 <requirements> 6 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">coverm</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">coverm</requirement>
5 </requirements> 8 </requirements>
6 </xml> 9 </xml>
7 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token> 10 <xml name="bio_tools">
8 <token name="@TOOL_VERSION@">0.6.1</token> 11 <xrefs>
9 <token name="@VERSION_SUFFIX@">0</token> 12 <xref type="bio.tools">coverm</xref>
10 <token name="@PROFILE@">22.01</token> 13 </xrefs>
14 </xml>
11 <xml name="citation"> 15 <xml name="citation">
12 <citations> 16 <citations>
13 <citation type="bibtex"> 17 <citation type="bibtex">
14 @misc{githubCoverm, 18 @misc{githubCoverm,
15 author = {B J. Woodcroft}, 19 author = {B J. Woodcroft},
20 url = {https://github.com/wwood/CoverM} 24 url = {https://github.com/wwood/CoverM}
21 } 25 }
22 </citation> 26 </citation>
23 </citations> 27 </citations>
24 </xml> 28 </xml>
25 <xml name="genome_opt"> 29 <xml name="mapped">
26 <conditional name="genome"> 30 <param name="mapped" type="select" label="Have the reads already been mapped to contigs?">
27 <param name="ref_or_genome" type="select" label="Select if you want to specify additional genome files."> 31 <option value="mapped">Yes (no read mapping algorithm will be undertaken)</option>
28 <option value="genomic">yes</option> 32 <option value="not-mapped" selected="true">No</option>
29 <option value="none" selected="true">No (Only when BAM files are provided)</option> 33 </param>
34 </xml>
35 <xml name="assembly_mode">
36 <param name="mode" type="select" label="Assembly mode?" help="Useful to know if contigs have been generated all samples together (co-assembly) or on each sample individually (individual assembly)">
37 <option value="individual">Individual assembly (1 contig file per sample)</option>
38 <option value="co" selected="true">Co-assembly (1 contig file for several samples)</option>
39 </param>
40 </xml>
41 <xml name="mapped_params">
42 <conditional name="mode">
43 <expand macro="assembly_mode"/>
44 <when value="individual">
45 <param argument="--bam-files" type="data" format="bam" label="BAM file(s)" help="These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n)."/>
46 </when>
47 <when value="co">
48 <param argument="--bam-files" type="data" format="bam" multiple="true" label="BAM file(s)" help="These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n)."/>
49 </when>
50 </conditional>
51 <param argument="--sharded" type="boolean" truevalue="--sharded" falsevalue="" checked="false" label="BAM file(s) read-sorted alignments of a set of reads mapped to multiple reference contig sets?" help="If set, it will choose the best hit for each read pair" />
52 </xml>
53 <token name="@BAMS@"><![CDATA[
54 #if $mapped.mode.mode == 'individual'
55 #set $fn = 'bam/' + re.sub('[^\s\w\-\\.]', '_', str($mapped.mode.bam_files.element_identifier))
56 #silent $bam_fp.append( $fn )
57 ln -s '$mapped.mode.bam_files' '$fn' &&
58 #else
59 #for $i, $bam in enumerate($mapped.mode.bam_files)
60 #set $fn = 'bam/' + re.sub('[^\s\w\-\\.]', '_', str($bam.element_identifier)) + '_' + str($i)
61 #silent $bam_fp.append( $fn )
62 ln -s '$bam' '$fn' &&
63 #end for
64 #end if
65 ]]></token>
66 <xml name="genomic">
67 <conditional name="genomic">
68 <param type="select" name="source" label="Source of FASTA files with each genome" >
69 <option value="history" selected="true">History</option>
70 <option value="builtin">Built-in</option>
30 </param> 71 </param>
31 <when value="none"> 72 <when value="history">
32 <param argument="--single-genome" type="boolean" truevalue="--single-genome" falsevalue="" checked="false" label="All contigs are from the same genome."/> 73 <param argument="--genome-fasta-files" type="data" format="fasta" multiple="true" label="FASTA files of each genome"/>
33 <param type="text" name="separator" optional="true" label="Character, that separates genome names from contig names in the reference file." > 74 </when>
34 <sanitizer> 75 <when value="builtin">
35 <valid initial="string.punctuation"> 76 <param argument="--genome-fasta-files" type="select" multiple="true" label="Reference genome(s)">
36 </valid> 77 <options from_data_table="all_fasta" />
37 </sanitizer>
38 </param> 78 </param>
39 </when> 79 </when>
40 <when value="genomic"> 80 </conditional>
41 <conditional name="genomic"> 81 </xml>
42 <param type="select" label="Reference genome source" name="source"> 82 <xml name="cond_single_genome">
43 <option value="history" selected="true">History</option> 83 <conditional name="cond_single_genome">
44 <option value="builtin">Built-in</option> 84 <param argument="--single-genome" type="select" label="Are all contigs from the same genome?">
85 <option value="--single-genome">True</option>
86 <option value="">False</option>
87 </param>
88 <when value="--single-genome"/>
89 <when value="">
90 <conditional name="genome_contig_definition">
91 <param argument="choice" type="select" label="How to get genome names and contig names?">
92 <option value="default" selected="true">Using default behavior</option>
93 <option value="genome-definition">Providing a file containing newline-separated list of genome name and contig</option>
94 <option value="separator">Providing character that separates genome names from contig names in the reference file</option>
45 </param> 95 </param>
46 <when value="history"> 96 <when value="default"/>
47 <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" /> 97 <when value="genome-definition">
98 <param argument="--genome-definition" type="data" format="tabular" label="File containing newline-separated list of genome_name and contig, separated by tab, to define the genome of each contig." />
48 </when> 99 </when>
49 <when value="builtin"> 100 <when value="separator">
50 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)"> 101 <param argument="--separator" type="text" label="Character that separates genome names from contig names in the reference file." >
51 <options from_data_table="all_fasta" />
52 </param>
53 </when>
54 </conditional>
55 </when>
56 </conditional>
57 </xml>
58 <xml name="genome">
59 <conditional name="genome">
60 <param name="ref_or_genome" type="select" label="Reference sequence mode" help="Select if you want to specify genome file(s) or a FASTA reference file or both. NOTE: If genomic FASTA files are specified, then reference is not needed as a reference FASTA file can be derived by concatenating input genomes. However, while not necessary, reference can be specified if an alternate reference sequence set is desired.">
61 <option value="genomic" selected="true">Reference genome</option>
62 <option value="reference">Contigs (e.g. concatenated genomes or metagenome assembly)</option>
63 </param>
64 <when value="genomic">
65 <conditional name="genomic">
66 <param type="select" label="Reference genome source" name="source">
67 <option value="history" selected="true">History</option>
68 <option value="builtin">Built-in</option>
69 </param>
70 <when value="history">
71 <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" />
72 </when>
73 <when value="builtin">
74 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)">
75 <options from_data_table="all_fasta" />
76 </param>
77 </when>
78 </conditional>
79 </when>
80 <when value="reference">
81 <param type="data" name="ref_source" multiple="true" label="Contigs file(s)" format="fasta" help="If multiple references FASTA files are provided and 'sharded' is specified, then reads will be mapped to references separately as sharded BAMs."/>
82 <conditional name="cond_single_genome">
83 <param name="single_genome" type="select" label="All contigs are from a single genome">
84 <option value="--single-genome">True</option>
85 <option value="false">False</option>
86 </param>
87 <when value="--single-genome">
88 <param type="data" name="genome_definition" format="tsv" optional="true" label="File containing newline-separated list of genome_name and contig, separated by tab, to define the genome of each contig." />
89 </when>
90 <when value="false">
91 <param type="text" argument="--separator" optional="true" label="Character, that separates genome names from contig names in the reference file." >
92 <sanitizer> 102 <sanitizer>
93 <valid initial="string.punctuation"> 103 <valid initial="string.punctuation">
94 </valid> 104 </valid>
95 </sanitizer> 105 </sanitizer>
96 </param> 106 </param>
97 </when> 107 </when>
98 </conditional>
99 <conditional name="add_genome">
100 <param name="add_genome" type="select" label="Add additional Genome Files">
101 <option value="true">Yes</option>
102 <option value="false" selected="true">No</option>
103 </param>
104 <when value="true">
105 <conditional name="add_genomic">
106 <param type="select" label="Reference genome source" name="source">
107 <option value="history" selected="true">History</option>
108 <option value="builtin">Built-in</option>
109 </param>
110 <when value="history">
111 <param type="data" name="fasta_history" multiple="true" label="Single FASTA file of contigs" format="fasta" />
112 </when>
113 <when value="builtin">
114 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome">
115 <options from_data_table="all_fasta" />
116 </param>
117 </when>
118 </conditional>
119 </when>
120 <when value="false">
121 </when>
122 </conditional> 108 </conditional>
123 </when> 109 </when>
124 </conditional> 110 </conditional>
125 </xml> 111 </xml>
126 <xml name="reads_for_contig"> 112 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>
127 <conditional name="reads"> 113 <xml name="read_type">
128 <param type="select" label="Read type" name="read_type"> 114 <param name="type" type="select" label="Read type" >
129 <option value="paired">Paired end</option> 115 <option value="single">Single end</option>
130 <option value="paired_collection" selected="true">Paired collection</option> 116 <option value="paired">Paired end</option>
131 <option value="single">Single ended</option> 117 <option value="paired_collection" selected="true">Paired collection</option>
132 <option value="interleaved">Interleaved</option> 118 <option value="interleaved">Interleaved</option>
133 <option value="bam">BAM file(s)</option> 119 </param>
134 </param> 120 </xml>
121 <xml name="paired_reads">
122 <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
123 </xml>
124 <xml name="individual_assembly_reads">
125 <conditional name="read_type">
126 <expand macro="read_type"/>
127 <when value="single">
128 <param argument="--single" type="data" format="@INPUT_FORMATS@" label="Single Read" />
129 </when>
135 <when value="paired"> 130 <when value="paired">
136 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" /> 131 <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" label="Forward FASTA/Q file for mapping" />
137 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" /> 132 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" label="Reverse FASTA/Q file for mapping" />
138 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
139 </when> 133 </when>
140 <when value="paired_collection"> 134 <when value="paired_collection">
141 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order" /> 135 <expand macro="paired_reads"/>
142 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> 136 </when>
143 </when> 137 <when value="interleaved">
138 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" label="Interleaved FASTA/Q files for mapping" />
139 </when>
140 </conditional>
141 </xml>
142 <xml name="ref_or_genome">
143 <param name="ref_or_genome" type="select" label="Genome definition">
144 <option value="contigs" selected="true">From contigs (e.g. concatenated genomes or metagenome assembly)</option>
145 <option value="genomic">From FASTA files with each genome</option>
146 </param>
147 </xml>
148 <xml name="individual_assembly_reference">
149 <param argument="--reference" type="data" format="fasta" label="Contigs"/>
150 </xml>
151 <token name="@INDIVIDUAL_ASSEMBLY_READS@"><![CDATA[
152 #set $reads = $mapped.mode.read_type
153 #if $reads.type == 'single'
154 #set $fn = "single/" + re.sub('[^\s\w\-\\.]', '_', str($reads.single.element_identifier))
155 #silent $single_fp.append( $fn )
156 ln -s '$reads.single' '$single_fp' &&
157 #else if $reads.type == 'paired'
158 #set $fn = "fw/" + re.sub('[^\s\w\-\\.]', '_', str($reads.read1.element_identifier))
159 #silent $fw_fp.append( $fn )
160 ln -s '$reads.read1' '$fn' &&
161 #set $fn = "rv/" + re.sub('[^\s\w\-\\.]', '_', str($reads.read2.element_identifier))
162 ln -s '$reads.read2' '$fn' &&
163 #silent $rv_fp.append( $fn )
164 #else if $reads.type == 'paired_collection'
165 #set $id = re.sub('[^\s\w\-\\.]', '_', str($reads.paired_reads.element_identifier))
166 #set $fn = "fw/" + $id
167 #silent $fw_fp.append( $fn )
168 ln -s '$reads.paired_reads.forward' '$fn' &&
169 #set $fn = "rv/" + $id
170 #silent $rv_fp.append( $fn )
171 ln -s '$mreads.paired_reads.reverse' '${fn}' &&
172 #else if $reads.type == 'interleaved'
173 #set $fn = "interl/" + re.sub('[^\s\w\-\\.]', '_', str($reads.interleaved.element_identifier))
174 #silent $interl_fp.append( $fn )
175 ln -s '$reads.interleaved' '$fn' &&
176 #end if
177 ]]></token>
178 <token name="@INDIVIDUAL_ASSEMBLY_REF@"><![CDATA[
179 #set $fn = "ref/" + re.sub('[^\s\w\-\\.]', '_', str($ref.element_identifier))
180 #silent $ref_fp.append( $fn )
181 ln -s '$ref' '${fn}' &&
182 ]]></token>
183 <token name="@GENOME_FOR_READS@"><![CDATA[
184 #if $mapped.mode.genome.genomic.source == 'history'
185 #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files)
186 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.element_identifier))
187 #silent $genome_fp.append( $fn )
188 ln -s '$genome' '$fn' &&
189 #end for
190 #else
191 #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files)
192 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.fields.path.element_identifier))
193 #silent $genome_fp.append( $fn )
194 ln -s '$genome' '$fn' &&
195 #end for
196 #end if
197 ]]></token>
198 <xml name="co_assembly_reads">
199 <conditional name="read_type">
200 <expand macro="read_type"/>
144 <when value="single"> 201 <when value="single">
145 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" /> 202 <param argument="--single" type="data" format="@INPUT_FORMATS@" multiple="true" label="Single Read" />
146 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> 203 </when>
204 <when value="paired">
205 <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" multiple="true" label="Forward FASTA/Q file(s) for mapping" />
206 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" multiple="true" label="Reverse FASTA/Q file(s) for mapping" />
207 </when>
208 <when value="paired_collection">
209 <expand macro="paired_reads"/>
147 </when> 210 </when>
148 <when value="interleaved"> 211 <when value="interleaved">
149 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" /> 212 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" multiple="true" label="Interleaved FASTA/Q files(s) for mapping" />
150 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> 213 </when>
151 </when> 214 </conditional>
152 <when value="bam"> 215 </xml>
153 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" help="BAM file(s). These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n). When specified, no read mapping algorithm is undertaken."/> 216 <xml name="co_assembly_reference">
154 <param type="data" name="ref_fasta_history" optional="true" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> 217 <param argument="--reference" type="data" format="fasta" multiple="true" label="Contigs" />
155 </when> 218 <param argument="--sharded" type="boolean" truevalue="--sharded" falsevalue="" checked="false" label="Mapping reads to references separately as sharded BAMs?" />
156 </conditional> 219 </xml>
157 </xml> 220 <token name="@CO_ASSEMBLY_READS@"><![CDATA[
158 <xml name="reads"> 221 #if $reads.type == 'single'
159 <conditional name="reads"> 222 #for $i, $read in enumerate($reads.single)
160 <param type="select" label="Read type" name="read_type"> 223 #set $fn = "single/" + re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) + "_single_" + str($i) + $extra
161 <option value="single">Single ended</option> 224 #silent $single_fp.append( $fn )
162 <option value="paired">Paired end</option> 225 ln -s '$read' '$fn' &&
163 <option value="paired_collection" selected="true">Paired collection</option> 226 #end for
164 <option value="interleaved">Interleaved</option> 227 #else if $reads.type == 'paired'
165 <option value="bam">BAM file(s)</option> 228 #for $i, $read in enumerate($reads.read1)
166 </param> 229 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
167 <when value="paired"> 230 #set $fn = "fw/" + $id + "_paired_" + str($i) + $extra
168 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" /> 231 #silent $fw_fp.append( $fn )
169 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" /> 232 ln -s '$read' '$fn' &&
170 <expand macro="genome"/> 233 #end for
171 </when> 234 #for $i, $read in enumerate($reads.read2)
172 <when value="paired_collection"> 235 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
173 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="Collection of paired-reads" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." /> 236 #set $fn = "rv/" + $id + "_paired_" + str($i) + $extra
174 <expand macro="genome"/> 237 #silent $rv_fp.append( $fn )
175 </when> 238 ln -s '$read' '$fn' &&
176 <when value="single"> 239 #end for
177 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" /> 240 #else if $reads.type == 'paired_collection'
178 <expand macro="genome"/> 241 #for $i, $read in enumerate($reads.paired_reads)
179 </when> 242 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
180 <when value="interleaved"> 243 #set $fn = "fw/" + $id + "_paired_collection_" + str($i) + $extra
181 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" /> 244 #silent $fw_fp.append( $fn )
182 <expand macro="genome"/> 245 ln -s '$read.forward' '$fn' &&
183 </when> 246 #set $fn = "rv/" + $id + "_paired_collection_" + str($i) + $extra
184 <when value="bam"> 247 #silent $rv_fp.append( $fn )
185 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" help="BAM file(s). These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n). When specified, no read mapping algorithm is undertaken."/> 248 ln -s '$read.reverse' '$fn' &&
186 <expand macro="genome_opt"/> 249 #end for
187 </when> 250 #else if $reads.type == 'interleaved'
188 </conditional> 251 #for $i, $read in enumerate($reads.interleaved)
189 </xml> 252 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
190 <xml name="add_reads"> 253 #set $fn = "interl/" + $id + "_interleaved_" + str($i) + $extra
191 <section name="add_reads" title="Add an additional read"> 254 #silent $interl_fp.append( $fn )
192 <conditional name="extra_read"> 255 ln -s '$read' '$fn' &&
193 <param type="select" label="Read type" name="read_type"> 256 #end for
194 <option value="none" selected="true">None</option> 257 #end if
195 <option value="paired">Paired end</option> 258 ]]></token>
196 <option value="paired_collection">Paired collection</option> 259 <token name="@CO_ASSEMBLY_ALL_READS@"><![CDATA[
197 <option value="single">Single ended</option> 260 #set $reads = $mapped.mode.read_type
198 <option value="interleaved">Interleaved</option> 261 #set $extra = ''
199 <option value="bam">BAM file(s)</option> 262 @CO_ASSEMBLY_READS@
200 </param> 263 #for $j, $s in enumerate($mapped.mode.extra_reads)
201 <when value="none"> 264 #set $reads = $s.read_type
202 </when> 265 #set $extra = str($j)
203 <when value="paired"> 266 @CO_ASSEMBLY_READS@
204 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" /> 267 #end for
205 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" /> 268 ]]></token>
206 </when> 269 <token name="@CO_ASSEMBLY_REF@"><![CDATA[
207 <when value="paired_collection"> 270 #for $i, $ref in enumerate($refs)
208 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order" /> 271 #set $fn = "ref/" + re.sub('[^\s\w\-\\.]', '_', str($ref.element_identifier)) + "_" + str($i)
209 </when> 272 #silent $ref_fp.append( $fn )
210 <when value="single"> 273 ln -s '$ref' '${fn}' &&
211 <param type="data" format="@INPUT_FORMATS@" name="single" multiple="true" label="Single read" /> 274 #end for
212 </when> 275 ]]></token>
213 <when value="interleaved"> 276 <xml name="sharded">
214 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" /> 277 <param name="sharded" type="boolean" truevalue="--sharded" falsevalue="" checked="false" label="Input BAM files are read-sorted alignments of a set of reads mapped to multiple reference contig sets. Choose the best hit for each read pair. Otherwise if mapping was carried out: Map reads to each reference, choosing the best hit for each pair." />
215 </when>
216 <when value="bam">
217 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" />
218 </when>
219 </conditional>
220 </section>
221 </xml> 278 </xml>
222 <xml name="mapping"> 279 <xml name="mapping">
223 <section name="mapping" title="Mapping options" expanded="false"> 280 <param argument="--mapper" type="select" label="Underlying mapping software used">
224 <param argument="--mapper" optional="true" type="select" label="Mapper" help="Underlying mapping software used. Default: minimap2-sr" > 281 <option value="minimap2-sr" selected="true">minimap2 with '-x sr' option</option>
225 <option value="minimap2-sr">minimap2 with '-x sr' option</option> 282 <option value="minimap2-ont">minimap2 with '-x map-ont' option</option>
226 <option value="minimap2-ont">minimap2 with '-x map-ont' option</option> 283 <option value="minimap2-pb">minimap2 with '-x map-pb' option</option>
227 <option value="minimap2-pb">minimap2 with '-x map-pb' option</option> 284 <option value="minimap2-no-preset">minimap2 with no '-x' option</option>
228 <option value="minimap2-no-preset">minimap2 with no '-x' option</option> 285 <option value="bwa-mem">BWA-MEM using default parameters</option>
229 <option value="bwa-mem">BWA-MEM using default parameters</option> 286 </param>
230 </param> 287 </xml>
231 <param argument="--min_read-aligned-length" type="integer" min="0" value="0" 288 <xml name="alignment">
232 label="Min read aligned length" help="Exclude reads with smaller numbers of aligned bases. Default: 0" /> 289 <section name="alignment" title="Alignment thresholding" expanded="false">
233 <param argument="--min_read-percent-identity" type="float" min="0" max="100" value="0" 290 <param argument="--min-read-aligned-length" type="integer" min="0" value="0"
234 label="Min read percent identity" help="Exclude reads by overall percent identity e.g. 95 for 95%. Default: 0" /> 291 label="Minimum number of aligned bases" help="Reads with smaller numbers of aligned bases will be excluded" />
235 <param argument="--min_read-aligned-percent" type="float" min="0" max="100" value="0" 292 <param argument="--min-read-percent-identity" type="float" min="0" max="100" value="0"
236 label="Min read aligned percentage" help="Exclude reads by percent aligned bases e.g. 95 means 95% 293 label="Minimum overall percent identity" help="Reads with lower overall percent identity will be excluded." />
237 of the read's bases must be aligned. Default: 0" /> 294 <param argument="--min-read-aligned-percent" type="float" min="0" max="100" value="0"
238 <param argument="--min_read-aligned-length-pair" type="integer" min="0" value="0" 295 label="Minimum aligned base percent" help="Reads with lower percent aligned bases will be excluded" />
239 label="Min read aligned length pair" help="Exclude pairs with smaller numbers of aligned bases. 296 <conditional name="proper_pairs_only">
240 Implies --proper-pairs-only. Default: 0" /> 297 <param argument="--proper-pairs-only" type="select" label="Require reads to be mapped as proper pairs?">
241 <param argument="--min_read-percent-identity-pair" type="float" min="0" max="100" value="0" 298 <option value="--proper-pairs-only">Yes</option>
242 label="Min read percent identity pair" help="Exclude pairs by overall percent identity e.g. 95 for 95%.
243 Implies --proper-pairs-only. Default: 0" />
244 <param argument="--min_read-aligned-percent-pair" type="float" min="0" max="100" value="0"
245 label="Min read aligned percentage pair" help="Exclude reads by percent aligned bases e.g. 95 means 95% of
246 the read's bases must be aligned. Implies --proper-pairs-only. Default: 0" />
247 <param argument="--proper-pairs-only" type="boolean" truevalue="--proper-pairs-only" falsevalue=""
248 label="Require reads to be mapped as proper pairs" help="Default: not set"/>
249 <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue=""
250 label="Exclude supplementary alignments" help="Default: not set"/>
251 </section>
252 </xml>
253 <xml name="coverage">
254 <section name="cov" title="Coverage calculation options" expanded="false">
255 <param name="relative_abundance" type="boolean" falsevalue="" truevalue="relative_abundance" label="Relative abundance (default)"/>
256 <param name="mean" type="boolean" falsevalue="" truevalue="mean" label="Mean"/>
257 <conditional name="cond_methods">
258 <param name="trimmed_mean" type="select" label="Trimmed mean">
259 <option value="trimmed_mean">Yes</option>
260 <option value="" selected="true">No</option> 299 <option value="" selected="true">No</option>
261 </param> 300 </param>
262 <when value="trimmed_mean"> 301 <when value="--proper-pairs-only">
263 <param name="trim_min" type="integer" min="0" value="5" label="Trim min" help="Remove this smallest fraction of positions when calculating trimmed_mean default: 5"/> 302 <param argument="--min_read-aligned-length-pair" type="integer" min="0" value="0"
264 <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/> 303 label="Minimum number of aligned bases for pairs" help="Pairs with smaller numbers of aligned bases will be excluded." />
304 <param argument="--min-read-percent-identity-pair" type="float" min="0" max="100" value="0"
305 label="Minimum overall percent identity pair for pairs" help="Pairs by lower overall percent identity will be excluded" />
306 <param argument="--min-read-aligned-percent-pair" type="float" min="0" max="100" value="0"
307 label="Minimum percent of read aligned bases for pair" help="Pairs with lower reads percent aligned bases will be excluded" />
265 </when> 308 </when>
266 <when value=""/> 309 <when value=""/>
267 </conditional> 310 </conditional>
268 <param name="covered_bases" type="boolean" falsevalue="" truevalue="covered_bases" label="Covered bases"/> 311 <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue="" checked="false"
269 <param name="covered_fraction" type="boolean" falsevalue="" truevalue="covered_fraction" label="Covered fraction"/> 312 label="Exclude supplementary alignments"/>
270 <param name="variance" type="boolean" falsevalue="" truevalue="variance" label="Variance"/>
271 <param name="length" type="boolean" falsevalue="" truevalue="length" label="Length"/>
272 <param name="count" type="boolean" falsevalue="" truevalue="count" label="Count"/>
273 <param name="metabat" type="boolean" falsevalue="" truevalue="metabat" label="MetaBAT"/>
274 <param name="coverage_histogram" type="boolean" falsevalue="" truevalue="coverage_histogram" label="Coverage histogram"/>
275 <param name="reads_per_base" type="boolean" falsevalue="" truevalue="reads_per_base" label="Reads per base"/>
276 <param name="rpkm" type="boolean" falsevalue="" truevalue="rpkm" label="RPKM"/>
277 <param name="tpm" type="boolean" falsevalue="" truevalue="tpm" label="TPKM"/>
278 <param name="min_covered_fraction" type="integer" min="0" optional="true"
279 label="Min covered fraction" help="Genomes with less coverage than this reported as having zero coverage. Default: 10"/>
280 <param name="contig_end_exclusion" type="integer" min="0" optional="true"
281 label="Contig end exclusion" help="Exclude bases at the ends of reference sequences from calculation. Default: 75"/>
282 </section> 313 </section>
283 </xml> 314 </xml>
284 <xml name="out"> 315 <xml name="cov_method_options">
285 <section name="out" title="Output options" expanded="false"> 316 <option value="trimmed_mean">trimmed_mean: Average number of aligned reads overlapping each position after removing the most deeply and shallow-ly covered positions. </option>
286 <param name="output_format" type="select" label="Shape of output" help="'Sparse' for long format, 'dense' for species-by-site. Default: dense]"> 317 <option value="coverage_histogram">coverage_histogram: Histogram of coverage depths</option>
287 <option value="dense" selected="true">Dense</option> 318 <option value="covered_bases">covered_bases: Number of bases covered by 1 or more reads</option>
288 <option value="sparse">Sparse</option> 319 <option value="variance">variance: Variance of coverage depths</option>
289 </param> 320 <option value="length">length: Length of each contig in base pairs</option>
290 <param name="no_zeros" type="boolean" truevalue="--no-zeros" falsevalue="" optional="true" label="Omit printing of genomes that have zero coverage" /> 321 <option value="count">count: Number of reads aligned toq each contig. Note that a single read may be aligned to multiple contigs with supplementary alignments</option>
291 <param argument="--dereplication-output-cluster-definition" type="boolean" truevalue="--dereplication-output-cluster-definition" falsevalue="" label="Output a file of representative TAB member lines." /> 322 <option value="metabat">metabat: ("MetaBAT adjusted coverage") Coverage as defined in Kang et al 2015</option>
292 <param argument="--dereplication-output-representative-fasta-directory-copy" type="boolean" truevalue="--dereplication-output-representative-fasta-directory-copy" falsevalue="" label="Output representative genomes" /> 323 <option value="reads_per_base">reads_per_base: Number of reads aligned divided by the length of the contig</option>
293 </section> 324 <option value="rpkm">rpkm: Reads mapped per kilobase of contig, per million mapped reads</option>
325 <option value="tpm">tpm: Transcripts Per Million as described in Li et al 2010</option>
326 </xml>
327 <xml name="coverage_params">
328 <param argument="--trim-min" type="integer" min="0" value="5" label="Smallest fraction of positions to remove when calculating" help="Only used with trimmed_mean method"/>
329 <param argument="--trim-max" type="integer" min="0" value="95" label="Maximum fraction of positions to remove when calculating" help="Only used with trimmed_mean method"/>
330 <param argument="--min-covered-fraction" type="integer" min="0" value="10" label="Minimum covered fraction" help="Genomes with less coverage than this reported as having zero coverage"/>
331 <param argument="--contig-end-exclusion" type="integer" min="0" value="75" label="Base to exclude at contig ends" help="Bases at the ends of reference sequences will be excluded from calculation"/>
332 </xml>
333 <xml name="output_format">
334 <param argument="--output-format" type="select" label="Shape of output">
335 <option value="dense" selected="true">Dense for species-by-site</option>
336 <option value="sparse">Sparse for long format</option>
337 </param>
294 </xml> 338 </xml>
295 <xml name="citations"> 339 <xml name="citations">
296 <citations> 340 <citations>
297 <yield /> 341 <yield />
298 </citations> 342 </citations>