Mercurial > repos > iuc > snpfreqplot

comparison snpfreqplot.xml @ 2:dc51db22310c 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/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
author iuc
date Fri, 18 Dec 2020 23:48:01 +0000
parents e362b3143cde
children 3d0adeee3f2b
comparison
equal deleted inserted replaced
1:e362b3143cde 2:dc51db22310c
1 <tool id="snpfreqplot" name="Variant Frequency Plot" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.09" 1 <tool id="snpfreqplot" name="Variant Frequency Plot" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.09"
2 license="GPL-3.0-or-later" > 2 license="GPL-3.0-or-later" >
3 <description>Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data</description> 3 <description>Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data</description>
4 <macros> 4 <macros>
5 <token name="@VERSION@">1.0</token> 5 <token name="@VERSION@">1.0</token>
6 <token name="@GALAXY_VERSION@">1</token> 6 <token name="@GALAXY_VERSION@">2</token>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="4.0">r-base</requirement> 9 <requirement type="package" version="4.0">r-base</requirement>
10 <requirement type="package" version="1.0.12">r-pheatmap</requirement> 10 <requirement type="package" version="1.0.12">r-pheatmap</requirement>
11 <requirement type="package" version="1.3.0">r-tidyverse</requirement> 11 <requirement type="package" version="1.3.0">r-tidyverse</requirement>
177 <!-- PDF, tabular inputs --> 177 <!-- PDF, tabular inputs -->
178 <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular,input443.tabular,input444.tabular" /> 178 <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular,input443.tabular,input444.tabular" />
179 <output name="outfile" ftype="pdf" value="heatmap.default.pdf" compare="sim_size" delta="250" /> 179 <output name="outfile" ftype="pdf" value="heatmap.default.pdf" compare="sim_size" delta="250" />
180 </test> 180 </test>
181 <test expect_num_outputs="1"> 181 <test expect_num_outputs="1">
182 <!-- PDF, tabular inputs, short color palette -->
183 <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular,input443.tabular,input444.tabular" />
184 <section name="advanced" >
185 <param name="color" value="Set2" />
186 </section>
187 <output name="outfile" ftype="pdf" value="heatmap.default.pdf" compare="sim_size" delta="250" />
188 </test>
189 <test expect_num_outputs="1">
182 <!-- PNG, multiple inputs, non-numeric IDS --> 190 <!-- PNG, multiple inputs, non-numeric IDS -->
183 <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input443.tabular,input444.tabular" /> 191 <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input443.tabular,input444.tabular" />
184 <param name="varfreq" value="0.5" /> 192 <param name="varfreq" value="0.5" />
185 <section name="advanced" > 193 <section name="advanced" >
186 <param name="color" value="Spectral" /> 194 <param name="color" value="Spectral" />
240 <has_text text="viewBox=&quot;0 0 754 292&quot;" /> 248 <has_text text="viewBox=&quot;0 0 754 292&quot;" />
241 </assert_contents> 249 </assert_contents>
242 </output> 250 </output>
243 </test> 251 </test>
244 <test expect_num_outputs="1"> 252 <test expect_num_outputs="1">
245 <!-- SVG, Vcf test with problematic splice+syn at snpeff789.vcf for threshold = 0.0222 --> 253 <!-- SVG, Vcf test with problematic splice+syn at snpeff789.vcf for threshold = 0.0222
246 <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf" /> 254 and an "empty" file (no variants) and a file with just one variant among its inputs -->
255 <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf,no_variants.vcf,single_variant.vcf" />
247 <param name="varfreq" value="0.0222" /> 256 <param name="varfreq" value="0.0222" />
248 <section name="advanced" > 257 <section name="advanced" >
249 <param name="output_type" value="svg" /> 258 <param name="output_type" value="svg" />
250 </section> 259 </section>
251 <output name="outfile" ftype="svg"> 260 <output name="outfile" ftype="svg">
252 <assert_contents> 261 <assert_contents>
253 <has_text text="viewBox=&quot;0 0 3101 879&quot;" /> 262 <has_text text="viewBox=&quot;0 0 1962 546&quot;" />
254 </assert_contents> 263 </assert_contents>
255 </output> 264 </output>
256 </test> 265 </test>
257 </tests> 266 </tests>
258 <help><![CDATA[ 267 <help><![CDATA[