Mercurial > repos > iuc > coverm_contig

comparison macros.xml @ 1:8b2b19eefc52 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
author iuc
date Tue, 24 Jan 2023 12:32:29 +0000
parents 4d15cbc3f077
children cc7863bec4e0
comparison
equal deleted inserted replaced
0:4d15cbc3f077 1:8b2b19eefc52
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=""/>