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comparison stacks_denovomap.xml @ 12:fdbcc560c691 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 22:03:44 +0000
parents 9f9d39f582f3
children
comparison
equal deleted inserted replaced
11:9f9d39f582f3 12:fdbcc560c691
1 <tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.0">
2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description> 2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 10
11 @CLEAN_EXT@ 11 @CLEAN_EXT@
171 </when> 171 </when>
172 </conditional> 172 </conditional>
173 173
174 <!-- stack assembly options --> 174 <!-- stack assembly options -->
175 <section name="assembly_options" title="Assembly options" expanded="false"> 175 <section name="assembly_options" title="Assembly options" expanded="false">
176 <param name="m" argument="-m" type="integer" value="" optional="true" label="Minimum number of identical raw reads required to create a stack" /> 176 <param argument="-m" type="integer" value="" optional="true" label="Minimum number of identical raw reads required to create a stack" />
177 <param name="P" argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" /> 177 <param argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" />
178 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/> 178 <param argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/>
179 <param name="N" argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" /> 179 <param argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" />
180 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog"/> 180 <param argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog"/>
181 181 <param argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" />
182 <param name="t" argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" /> 182 <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
183 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
184 </section> 183 </section>
185 184
186 <!-- SNP Model options --> 185 <!-- SNP Model options -->
187 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False"> 186 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
188 <expand macro="snp_options"/> 187 <expand macro="snp_options"/>
189 </section> 188 </section>
190 </inputs> 189 </inputs>
191 <outputs> 190 <outputs>
192 <data format="txt" name="output_log" label="denovo_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/denovo_map.log" /> 191 <data format="txt" name="output_log" label="denovo_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/denovo_map.log" />
193
194 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" /> 192 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
195
196 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" /> 193 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
197 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" /> 194 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
198 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" /> 195 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
199
200 <expand macro="genotypes_output_light"/> 196 <expand macro="genotypes_output_light"/>
201 <expand macro="populations_output_light"/> 197 <expand macro="populations_output_light"/>
202
203 <collection name="tags" type="list" label="Assembled loci from ${on_string}"> 198 <collection name="tags" type="list" label="Assembled loci from ${on_string}">
204 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> 199 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
205 </collection> 200 </collection>
206
207 <collection name="snps" type="list" label="Model calls from each locus on ${on_string}"> 201 <collection name="snps" type="list" label="Model calls from each locus on ${on_string}">
208 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> 202 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
209 </collection> 203 </collection>
210
211 <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus on ${on_string}"> 204 <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus on ${on_string}">
212 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> 205 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
213 </collection> 206 </collection>
214
215 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}"> 207 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
216 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> 208 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
217 </collection> 209 </collection>
218
219 <collection name="all_output" type="list" label="Full output from denovo_map on ${on_string}"> 210 <collection name="all_output" type="list" label="Full output from denovo_map on ${on_string}">
220 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles|matches))\.tsv$" ext="tabular" directory="stacks_outputs" /> 211 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles|matches))\.tsv$" ext="tabular" directory="stacks_outputs" />
221 <discover_datasets pattern="(?P&lt;name&gt;.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv$" ext="tabular" directory="stacks_outputs" /> 212 <discover_datasets pattern="(?P&lt;name&gt;.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv$" ext="tabular" directory="stacks_outputs" />
222 <discover_datasets pattern="(?P&lt;name&gt;.+\.(genotypes))\.(loc|txt)$" ext="txt" directory="stacks_outputs" /> 213 <discover_datasets pattern="(?P&lt;name&gt;.+\.(genotypes))\.(loc|txt)$" ext="txt" directory="stacks_outputs" />
223 </collection> 214 </collection>