Mercurial > repos > iuc > coverm_contig
comparison macros.xml @ 1:688a777e1b19 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
author | iuc |
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date | Tue, 24 Jan 2023 12:33:11 +0000 |
parents | 6941d0d453ba |
children | c2a5823e4763 |
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0:6941d0d453ba | 1:688a777e1b19 |
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1 <macros> | 1 <macros> |
2 <xml name="requirements"> | 2 <xml name="requirements"> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package">coverm</requirement> | 4 <requirement type="package" version="@TOOL_VERSION@">coverm</requirement> |
5 </requirements> | 5 </requirements> |
6 </xml> | 6 </xml> |
7 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token> | 7 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token> |
8 <token name="@TOOL_VERSION@">0.2.1</token> | 8 <token name="@TOOL_VERSION@">0.6.1</token> |
9 <token name="@VERSION_SUFFIX@">0</token> | 9 <token name="@VERSION_SUFFIX@">0</token> |
10 <token name="@PROFILE@">22.01</token> | |
10 <xml name="citation"> | 11 <xml name="citation"> |
11 <citations> | 12 <citations> |
12 <citation type="bibtex"> | 13 <citation type="bibtex"> |
13 @misc{githubCoverm, | 14 @misc{githubCoverm, |
14 author = {B J. Woodcroft}, | 15 author = {B J. Woodcroft}, |
94 </sanitizer> | 95 </sanitizer> |
95 </param> | 96 </param> |
96 </when> | 97 </when> |
97 </conditional> | 98 </conditional> |
98 <conditional name="add_genome"> | 99 <conditional name="add_genome"> |
99 <param name="add_genome" type="boolean" label="Add additional Genome Files"/> | 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> | |
100 <when value="true"> | 104 <when value="true"> |
101 <conditional name="add_genomic"> | 105 <conditional name="add_genomic"> |
102 <param type="select" label="Reference genome source" name="source"> | 106 <param type="select" label="Reference genome source" name="source"> |
103 <option value="history" selected="true">History</option> | 107 <option value="history" selected="true">History</option> |
104 <option value="builtin">Built-in</option> | 108 <option value="builtin">Built-in</option> |
184 </conditional> | 188 </conditional> |
185 </xml> | 189 </xml> |
186 <xml name="add_reads"> | 190 <xml name="add_reads"> |
187 <section name="add_reads" title="Add an additional read"> | 191 <section name="add_reads" title="Add an additional read"> |
188 <conditional name="extra_read"> | 192 <conditional name="extra_read"> |
189 <param type="select" label="Read type" optional="true" name="read_type"> | 193 <param type="select" label="Read type" name="read_type"> |
190 <option value="none" selected="true">None</option> | 194 <option value="none" selected="true">None</option> |
191 <option value="paired">Paired end</option> | 195 <option value="paired">Paired end</option> |
192 <option value="paired_collection">Paired collection</option> | 196 <option value="paired_collection">Paired collection</option> |
193 <option value="single">Single ended</option> | 197 <option value="single">Single ended</option> |
194 <option value="interleaved">Interleaved</option> | 198 <option value="interleaved">Interleaved</option> |
249 <xml name="coverage"> | 253 <xml name="coverage"> |
250 <section name="cov" title="Coverage calculation options" expanded="false"> | 254 <section name="cov" title="Coverage calculation options" expanded="false"> |
251 <param name="relative_abundance" type="boolean" falsevalue="" truevalue="relative_abundance" label="Relative abundance (default)"/> | 255 <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"/> | 256 <param name="mean" type="boolean" falsevalue="" truevalue="mean" label="Mean"/> |
253 <conditional name="cond_methods"> | 257 <conditional name="cond_methods"> |
254 <param name="trimmed_mean" type="boolean" falsevalue="" truevalue="trimmed_mean" label="Trimmed mean"/> | 258 <param name="trimmed_mean" type="select" label="Trimmed mean"> |
259 <option value="trimmed_mean">Yes</option> | |
260 <option value="" selected="true">No</option> | |
261 </param> | |
255 <when value="trimmed_mean"> | 262 <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"/> | 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"/> |
257 <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/> | 264 <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/> |
258 </when> | 265 </when> |
259 <when value=""/> | 266 <when value=""/> |