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comparison macros.xml @ 0:4d15cbc3f077 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
author iuc
date Tue, 26 Apr 2022 15:25:50 +0000
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children 8b2b19eefc52
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-1:000000000000 0:4d15cbc3f077
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package">coverm</requirement>
5 </requirements>
6 </xml>
7 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>
8 <token name="@TOOL_VERSION@">0.2.1</token>
9 <token name="@VERSION_SUFFIX@">0</token>
10 <xml name="citation">
11 <citations>
12 <citation type="bibtex">
13 @misc{githubCoverm,
14 author = {B J. Woodcroft},
15 year = {2021},
16 title = {CoverM},
17 publisher = {GitHub},
18 journal = {GitHub repository},
19 url = {https://github.com/wwood/CoverM}
20 }
21 </citation>
22 </citations>
23 </xml>
24 <xml name="genome_opt">
25 <conditional name="genome">
26 <param name="ref_or_genome" type="select" label="Select if you want to specify additional genome files.">
27 <option value="genomic">yes</option>
28 <option value="none" selected="true">No (Only when BAM files are provided)</option>
29 </param>
30 <when value="none">
31 <param argument="--single-genome" type="boolean" truevalue="--single-genome" falsevalue="" checked="false" label="All contigs are from the same genome."/>
32 <param type="text" name="separator" optional="true" label="Character, that separates genome names from contig names in the reference file." >
33 <sanitizer>
34 <valid initial="string.punctuation">
35 </valid>
36 </sanitizer>
37 </param>
38 </when>
39 <when value="genomic">
40 <conditional name="genomic">
41 <param type="select" label="Reference genome source" name="source">
42 <option value="history" selected="true">History</option>
43 <option value="builtin">Built-in</option>
44 </param>
45 <when value="history">
46 <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" />
47 </when>
48 <when value="builtin">
49 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)">
50 <options from_data_table="all_fasta" />
51 </param>
52 </when>
53 </conditional>
54 </when>
55 </conditional>
56 </xml>
57 <xml name="genome">
58 <conditional name="genome">
59 <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.">
60 <option value="genomic" selected="true">Reference genome</option>
61 <option value="reference">Contigs (e.g. concatenated genomes or metagenome assembly)</option>
62 </param>
63 <when value="genomic">
64 <conditional name="genomic">
65 <param type="select" label="Reference genome source" name="source">
66 <option value="history" selected="true">History</option>
67 <option value="builtin">Built-in</option>
68 </param>
69 <when value="history">
70 <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" />
71 </when>
72 <when value="builtin">
73 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)">
74 <options from_data_table="all_fasta" />
75 </param>
76 </when>
77 </conditional>
78 </when>
79 <when value="reference">
80 <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."/>
81 <conditional name="cond_single_genome">
82 <param name="single_genome" type="select" label="All contigs are from a single genome">
83 <option value="--single-genome">True</option>
84 <option value="false">False</option>
85 </param>
86 <when value="--single-genome">
87 <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." />
88 </when>
89 <when value="false">
90 <param type="text" argument="--separator" optional="true" label="Character, that separates genome names from contig names in the reference file." >
91 <sanitizer>
92 <valid initial="string.punctuation">
93 </valid>
94 </sanitizer>
95 </param>
96 </when>
97 </conditional>
98 <conditional name="add_genome">
99 <param name="add_genome" type="boolean" label="Add additional Genome Files"/>
100 <when value="true">
101 <conditional name="add_genomic">
102 <param type="select" label="Reference genome source" name="source">
103 <option value="history" selected="true">History</option>
104 <option value="builtin">Built-in</option>
105 </param>
106 <when value="history">
107 <param type="data" name="fasta_history" multiple="true" label="Single FASTA file of contigs" format="fasta" />
108 </when>
109 <when value="builtin">
110 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome">
111 <options from_data_table="all_fasta" />
112 </param>
113 </when>
114 </conditional>
115 </when>
116 <when value="false">
117 </when>
118 </conditional>
119 </when>
120 </conditional>
121 </xml>
122 <xml name="reads_for_contig">
123 <conditional name="reads">
124 <param type="select" label="Read type" name="read_type">
125 <option value="paired">Paired end</option>
126 <option value="paired_collection" selected="true">Paired collection</option>
127 <option value="single">Single ended</option>
128 <option value="interleaved">Interleaved</option>
129 <option value="bam">BAM file(s)</option>
130 </param>
131 <when value="paired">
132 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" />
133 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" />
134 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
135 </when>
136 <when value="paired_collection">
137 <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" />
138 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
139 </when>
140 <when value="single">
141 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" />
142 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
143 </when>
144 <when value="interleaved">
145 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" />
146 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
147 </when>
148 <when value="bam">
149 <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."/>
150 <param type="data" name="ref_fasta_history" optional="true" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
151 </when>
152 </conditional>
153 </xml>
154 <xml name="reads">
155 <conditional name="reads">
156 <param type="select" label="Read type" name="read_type">
157 <option value="single">Single ended</option>
158 <option value="paired">Paired end</option>
159 <option value="paired_collection" selected="true">Paired collection</option>
160 <option value="interleaved">Interleaved</option>
161 <option value="bam">BAM file(s)</option>
162 </param>
163 <when value="paired">
164 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" />
165 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" />
166 <expand macro="genome"/>
167 </when>
168 <when value="paired_collection">
169 <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." />
170 <expand macro="genome"/>
171 </when>
172 <when value="single">
173 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" />
174 <expand macro="genome"/>
175 </when>
176 <when value="interleaved">
177 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" />
178 <expand macro="genome"/>
179 </when>
180 <when value="bam">
181 <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."/>
182 <expand macro="genome_opt"/>
183 </when>
184 </conditional>
185 </xml>
186 <xml name="add_reads">
187 <section name="add_reads" title="Add an additional read">
188 <conditional name="extra_read">
189 <param type="select" label="Read type" optional="true" name="read_type">
190 <option value="none" selected="true">None</option>
191 <option value="paired">Paired end</option>
192 <option value="paired_collection">Paired collection</option>
193 <option value="single">Single ended</option>
194 <option value="interleaved">Interleaved</option>
195 <option value="bam">BAM file(s)</option>
196 </param>
197 <when value="none">
198 </when>
199 <when value="paired">
200 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" />
201 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" />
202 </when>
203 <when value="paired_collection">
204 <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" />
205 </when>
206 <when value="single">
207 <param type="data" format="@INPUT_FORMATS@" name="single" multiple="true" label="Single read" />
208 </when>
209 <when value="interleaved">
210 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" />
211 </when>
212 <when value="bam">
213 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" />
214 </when>
215 </conditional>
216 </section>
217 </xml>
218 <xml name="mapping">
219 <section name="mapping" title="Mapping options" expanded="false">
220 <param argument="--mapper" optional="true" type="select" label="Mapper" help="Underlying mapping software used. Default: minimap2-sr" >
221 <option value="minimap2-sr">minimap2 with '-x sr' option</option>
222 <option value="minimap2-ont">minimap2 with '-x map-ont' option</option>
223 <option value="minimap2-pb">minimap2 with '-x map-pb' option</option>
224 <option value="minimap2-no-preset">minimap2 with no '-x' option</option>
225 <option value="bwa-mem">BWA-MEM using default parameters</option>
226 </param>
227 <param argument="--min_read-aligned-length" type="integer" min="0" value="0"
228 label="Min read aligned length" help="Exclude reads with smaller numbers of aligned bases. Default: 0" />
229 <param argument="--min_read-percent-identity" type="float" min="0" max="100" value="0"
230 label="Min read percent identity" help="Exclude reads by overall percent identity e.g. 95 for 95%. Default: 0" />
231 <param argument="--min_read-aligned-percent" type="float" min="0" max="100" value="0"
232 label="Min read aligned percentage" help="Exclude reads by percent aligned bases e.g. 95 means 95%
233 of the read's bases must be aligned. Default: 0" />
234 <param argument="--min_read-aligned-length-pair" type="integer" min="0" value="0"
235 label="Min read aligned length pair" help="Exclude pairs with smaller numbers of aligned bases.
236 Implies --proper-pairs-only. Default: 0" />
237 <param argument="--min_read-percent-identity-pair" type="float" min="0" max="100" value="0"
238 label="Min read percent identity pair" help="Exclude pairs by overall percent identity e.g. 95 for 95%.
239 Implies --proper-pairs-only. Default: 0" />
240 <param argument="--min_read-aligned-percent-pair" type="float" min="0" max="100" value="0"
241 label="Min read aligned percentage pair" help="Exclude reads by percent aligned bases e.g. 95 means 95% of
242 the read's bases must be aligned. Implies --proper-pairs-only. Default: 0" />
243 <param argument="--proper-pairs-only" type="boolean" truevalue="--proper-pairs-only" falsevalue=""
244 label="Require reads to be mapped as proper pairs" help="Default: not set"/>
245 <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue=""
246 label="Exclude supplementary alignments" help="Default: not set"/>
247 </section>
248 </xml>
249 <xml name="coverage">
250 <section name="cov" title="Coverage calculation options" expanded="false">
251 <param name="relative_abundance" type="boolean" falsevalue="" truevalue="relative_abundance" label="Relative abundance (default)"/>
252 <param name="mean" type="boolean" falsevalue="" truevalue="mean" label="Mean"/>
253 <conditional name="cond_methods">
254 <param name="trimmed_mean" type="boolean" falsevalue="" truevalue="trimmed_mean" label="Trimmed mean"/>
255 <when value="trimmed_mean">
256 <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"/>
257 <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/>
258 </when>
259 <when value=""/>
260 </conditional>
261 <param name="covered_bases" type="boolean" falsevalue="" truevalue="covered_bases" label="Covered bases"/>
262 <param name="covered_fraction" type="boolean" falsevalue="" truevalue="covered_fraction" label="Covered fraction"/>
263 <param name="variance" type="boolean" falsevalue="" truevalue="variance" label="Variance"/>
264 <param name="length" type="boolean" falsevalue="" truevalue="length" label="Length"/>
265 <param name="count" type="boolean" falsevalue="" truevalue="count" label="Count"/>
266 <param name="metabat" type="boolean" falsevalue="" truevalue="metabat" label="MetaBAT"/>
267 <param name="coverage_histogram" type="boolean" falsevalue="" truevalue="coverage_histogram" label="Coverage histogram"/>
268 <param name="reads_per_base" type="boolean" falsevalue="" truevalue="reads_per_base" label="Reads per base"/>
269 <param name="rpkm" type="boolean" falsevalue="" truevalue="rpkm" label="RPKM"/>
270 <param name="tpm" type="boolean" falsevalue="" truevalue="tpm" label="TPKM"/>
271 <param name="min_covered_fraction" type="integer" min="0" optional="true"
272 label="Min covered fraction" help="Genomes with less coverage than this reported as having zero coverage. Default: 10"/>
273 <param name="contig_end_exclusion" type="integer" min="0" optional="true"
274 label="Contig end exclusion" help="Exclude bases at the ends of reference sequences from calculation. Default: 75"/>
275 </section>
276 </xml>
277 <xml name="out">
278 <section name="out" title="Output options" expanded="false">
279 <param name="output_format" type="select" label="Shape of output" help="'Sparse' for long format, 'dense' for species-by-site. Default: dense]">
280 <option value="dense" selected="true">Dense</option>
281 <option value="sparse">Sparse</option>
282 </param>
283 <param name="no_zeros" type="boolean" truevalue="--no-zeros" falsevalue="" optional="true" label="Omit printing of genomes that have zero coverage" />
284 <param argument="--dereplication-output-cluster-definition" type="boolean" truevalue="--dereplication-output-cluster-definition" falsevalue="" label="Output a file of representative TAB member lines." />
285 <param argument="--dereplication-output-representative-fasta-directory-copy" type="boolean" truevalue="--dereplication-output-representative-fasta-directory-copy" falsevalue="" label="Output representative genomes" />
286 </section>
287 </xml>
288 <xml name="citations">
289 <citations>
290 <yield />
291 </citations>
292 </xml>
293 </macros>