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comparison snpfreqplot.xml @ 1:480821a403a0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"
author iuc
date Thu, 10 Dec 2020 13:41:00 +0000
parents 469cc3aadaa7
children 59a7bb93b5fe
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0:469cc3aadaa7 1:480821a403a0
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@">0</token> 6 <token name="@GALAXY_VERSION@">1</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>
12 <requirement type="package" version="1.36.0">bioconductor-variantannotation</requirement> 12 <requirement type="package" version="1.36.0">bioconductor-variantannotation</requirement>
13 <requirement type="package" version="">xorg-libxt</requirement>
14 </requirements> 13 </requirements>
15 <edam_topics> 14 <edam_topics>
16 <edam_topic>topic_0797</edam_topic> 15 <edam_topic>topic_0797</edam_topic>
17 <edam_topic>topic_0092</edam_topic> 16 <edam_topic>topic_0092</edam_topic>
18 </edam_topics> 17 </edam_topics>
185 <param name="varfreq" value="0.5" /> 184 <param name="varfreq" value="0.5" />
186 <section name="advanced" > 185 <section name="advanced" >
187 <param name="color" value="Spectral" /> 186 <param name="color" value="Spectral" />
188 <param name="output_type" value="png" /> 187 <param name="output_type" value="png" />
189 </section> 188 </section>
190 <output name="outfile" ftype="png" value="heatmap.imageopts.png" compare="sim_size" delta="86000" /> 189 <output name="outfile" ftype="png" value="heatmap.imageopts.png" compare="sim_size" delta="100000" />
191 </test> 190 </test>
192 <test expect_num_outputs="1"> 191 <test expect_num_outputs="1">
193 <!-- SVG, clustering defaults --> 192 <!-- SVG, clustering defaults -->
194 <param name="sinputs" ftype="tabular" value="input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular" /> 193 <param name="sinputs" ftype="tabular" value="input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular" />
195 <conditional name="clustering"> 194 <conditional name="clustering">
200 <param name="ratio" value="0.8" /> 199 <param name="ratio" value="0.8" />
201 <param name="output_type" value="svg" /> 200 <param name="output_type" value="svg" />
202 </section> 201 </section>
203 <output name="outfile" ftype="svg"> 202 <output name="outfile" ftype="svg">
204 <assert_contents> 203 <assert_contents>
205 <has_text text="viewBox=&quot;0 0 1156 335&quot;" /> 204 <has_text text="viewBox=&quot;0 0 1156 361&quot;" />
206 </assert_contents> 205 </assert_contents>
207 </output> 206 </output>
208 </test> 207 </test>
209 <test expect_num_outputs="1"> 208 <test expect_num_outputs="1">
210 <!-- JPEG, clustering extras, mixed alphanumeric labels --> 209 <!-- JPEG, clustering extras, mixed alphanumeric labels -->
217 <section name="advanced" > 216 <section name="advanced" >
218 <param name="color" value="Purples" /> 217 <param name="color" value="Purples" />
219 <param name="ratio" value="1.2" /> 218 <param name="ratio" value="1.2" />
220 <param name="output_type" value="jpeg" /> 219 <param name="output_type" value="jpeg" />
221 </section> 220 </section>
222 <output name="outfile" ftype="jpg" value="heatmap.clustering2.jpeg" compare="sim_size" delta="121000" /> 221 <output name="outfile" ftype="jpg" value="heatmap.clustering2.jpeg" compare="sim_size" delta="130000" />
223 </test> 222 </test>
224 <test expect_num_outputs="1"> 223 <test expect_num_outputs="1">
225 <!-- PDF, vcf test --> 224 <!-- PDF, vcf test -->
226 <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf" /> 225 <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf" />
227 <section name="advanced" > 226 <section name="advanced" >
236 <section name="advanced" > 235 <section name="advanced" >
237 <param name="output_type" value="svg" /> 236 <param name="output_type" value="svg" />
238 </section> 237 </section>
239 <output name="outfile" ftype="svg"> 238 <output name="outfile" ftype="svg">
240 <assert_contents> 239 <assert_contents>
241 <has_text text="viewBox=&quot;0 0 754 271&quot;" /> 240 <has_text text="viewBox=&quot;0 0 754 292&quot;" />
242 </assert_contents> 241 </assert_contents>
243 </output> 242 </output>
244 </test> 243 </test>
245 <test expect_num_outputs="1"> 244 <test expect_num_outputs="1">
246 <!-- SVG, Vcf test with problematic splice+syn at snpeff789.vcf for threshold = 0.0222 --> 245 <!-- SVG, Vcf test with problematic splice+syn at snpeff789.vcf for threshold = 0.0222 -->
249 <section name="advanced" > 248 <section name="advanced" >
250 <param name="output_type" value="svg" /> 249 <param name="output_type" value="svg" />
251 </section> 250 </section>
252 <output name="outfile" ftype="svg"> 251 <output name="outfile" ftype="svg">
253 <assert_contents> 252 <assert_contents>
254 <has_text text="viewBox=&quot;0 0 3101 697&quot;" /> 253 <has_text text="viewBox=&quot;0 0 3101 879&quot;" />
255 </assert_contents> 254 </assert_contents>
256 </output> 255 </output>
257 </test> 256 </test>
258 </tests> 257 </tests>
259 <help><![CDATA[ 258 <help><![CDATA[
289 - ``EFF[*].GENE`` 288 - ``EFF[*].GENE``
290 - ``EFF[*].EFFECT`` 289 - ``EFF[*].EFFECT``
291 290
292 Such files can be produced with SnpSift Extract Fields and can be useful if 291 Such files can be produced with SnpSift Extract Fields and can be useful if
293 preprocessing of the lists with standard text processing tools is required. 292 preprocessing of the lists with standard text processing tools is required.
293
294 .. class:: infomark
295
296 To represent empty EFF fields in the tabular format you can choose between
297 ``.`` and the empty string.
294 298
295 ---- 299 ----
296 300
297 Example output: 301 Example output:
298 302