Mercurial > repos > iuc > stacks2_shortreads

comparison macros.xml @ 5:4e280b27a831 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
author iuc
date Thu, 14 Apr 2022 09:25:46 +0000
parents 17d39bf0a63a
children 97575d01f06b
comparison
equal deleted inserted replaced
4:17d39bf0a63a 5:4e280b27a831
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@STACKS_VERSION@">stacks</requirement> 5 <requirement type="package" version="@TOOL_VERSION@">stacks</requirement>
6 <requirement type="package" version="3.7">python</requirement> 6 <requirement type="package" version="3.7">python</requirement>
7 <requirement type="package" version="4.6.0">findutils</requirement> 7 <requirement type="package" version="4.6.0">findutils</requirement>
8 <yield/> 8 <yield/>
9 </requirements> 9 </requirements>
10 </xml> 10 </xml>
11 11
12 <token name="@STACKS_VERSION@">2.55</token> 12 <token name="@TOOL_VERSION@">2.55</token>
13 <token name="@WRAPPER_VERSION@">1</token> 13 <token name="@VERSION_SUFFIX@">2</token>
14 <token name="@PROFILE@">20.05</token> 14 <token name="@PROFILE@">20.05</token>
15 15
16 <xml name="citation"> 16 <xml name="citation">
17 <citations> 17 <citations>
18 <citation type="doi">10.1111/mec.12354</citation> 18 <citation type="doi">10.1111/mec.12354</citation>
215 <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@"> 215 <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@">
216 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file"/> 216 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file"/>
217 </expand> 217 </expand>
218 </xml> 218 </xml>
219 219
220
221 <xml name="barcode_selector">
222 <param name="barcode_encoding" type="select" label="Barcode location">
223 <option value="">Disabled</option>
224 <yield/>
225 </param>
226 <param name="barcode" argument="-b" type="data" format="tabular,txt" optional="true" label="Barcode file" help="The barcode file is only used if barcode_input"/>
227 </xml>
228
229
220 <!-- fastq input (used in denovomap, tsv2bam, ustacks) 230 <!-- fastq input (used in denovomap, tsv2bam, ustacks)
221 - fastq_optional: makes fastq input optional (true/false) 231 - fastq_optional: makes fastq input optional (true/false)
222 - se_option: wording for "single end" option (for tsv2bam this is the 232 - se_option: wording for "single end" option (for tsv2bam this is the
223 reverse reads for the others its the forward reads) 233 reverse reads for the others its the forward reads)
224 - help: help text --> 234 - help: help text -->
225 <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help=""> 235 <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="" token_multiple="false" token_listtype="paired">
226 <conditional name="input_type"> 236 <conditional name="input_type">
227 <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@"> 237 <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@">
228 <option value="single" selected="true">@SE_OPTION@</option> 238 <option value="single" selected="true">@SE_OPTION@</option>
229 <option value="paired">(paired) dataset list</option> 239 <option value="paired">(paired) dataset list</option>
230 </param> 240 </param>
231 <when value="single"> 241 <when value="single">
232 <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/> 242 <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="@MULTIPLE@" optional="@FASTQ_OPTIONAL@"/>
233 </when> 243 </when>
234 <when value="paired"> 244 <when value="paired">
235 <param name="fqinputs" argument="-f" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/> 245 <param name="fqinputs" argument="-f" type="data_collection" collection_type="@LISTTYPE@" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/>
236 </when> 246 </when>
237 </conditional> 247 </conditional>
238 </xml> 248 </xml>
239 249
240 <!-- helper functions for linking fastq data sets --> 250 <!-- helper functions for linking fastq data sets -->