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comparison dropletutils.xml @ 4:1797cbe967d1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 49840f36c6623746bb7f8eb64bf4bf0cdae9c24e"
author iuc
date Thu, 05 Dec 2019 01:32:29 -0500
parents f0de368eabca
children cdf4443d5625
comparison
equal deleted inserted replaced
3:f0de368eabca 4:1797cbe967d1
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="dropletutils" name="DropletUtils" version="@PACKAGE_VERSION@+@GALAXY_VERSION@" > 2 <tool id="dropletutils" name="DropletUtils" version="@PACKAGE_VERSION@+@GALAXY_VERSION@" >
3 <description>Utilities for handling droplet-based single-cell RNA-seq data</description> 3 <description>Utilities for handling droplet-based single-cell RNA-seq data</description>
4 <macros> 4 <macros>
5 <token name="@PACKAGE_VERSION@" >1.2.1</token> 5 <token name="@PACKAGE_VERSION@" >1.2.1</token>
6 <token name="@GALAXY_VERSION@" >4</token> 6 <token name="@GALAXY_VERSION@" >5</token>
7 <token name="@TXIN@">tenx.input</token> 7 <token name="@TXIN@">tenx.input</token>
8 <token name="@TXOUT@">tenx.output</token> 8 <token name="@TXOUT@">tenx.output</token>
9 <xml name="test_dirin" > 9 <xml name="test_dirin" >
10 <conditional name="tenx_format"> 10 <conditional name="tenx_format">
11 <param name="use" value="directory" /> 11 <param name="use" value="directory" />
17 </macros> 17 </macros>
18 <requirements> 18 <requirements>
19 <requirement type="package" version="@PACKAGE_VERSION@">bioconductor-dropletutils</requirement> 19 <requirement type="package" version="@PACKAGE_VERSION@">bioconductor-dropletutils</requirement>
20 <requirement type="package" version="1.2_17" >r-matrix</requirement> 20 <requirement type="package" version="1.2_17" >r-matrix</requirement>
21 <requirement type="package" version="1.10.1" >bioconductor-scater</requirement> 21 <requirement type="package" version="1.10.1" >bioconductor-scater</requirement>
22 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
22 </requirements> 23 </requirements>
23 <version_command><![CDATA[ 24 <version_command><![CDATA[
24 Rscript -e 'packageVersion("DropletUtils")' | grep -oP '\d\.\d\.\d' 25 Rscript -e 'packageVersion("DropletUtils")' | grep -oP '\d\.\d\.\d'
25 ]]> 26 ]]>
26 </version_command> 27 </version_command>
200 <expand macro="test_dirin" /> 201 <expand macro="test_dirin" />
201 <conditional name="operation"> 202 <conditional name="operation">
202 <param name="use" value="barcode_rank" /> 203 <param name="use" value="barcode_rank" />
203 <param name="lower" value="120" /> 204 <param name="lower" value="120" />
204 </conditional> 205 </conditional>
205 <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="200"/> 206 <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="400"/>
206 </test> 207 </test>
207 <!-- ::: Empty Drops --> 208 <!-- ::: Empty Drops -->
208 <test expect_num_outputs="3"> 209 <test expect_num_outputs="3">
209 <expand macro="test_dirin" /> 210 <expand macro="test_dirin" />
210 <conditional name="operation"> 211 <conditional name="operation">
223 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> 224 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
224 <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" /> 225 <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
225 <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166.644236503983\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" /> 226 <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166.644236503983\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
226 </assert_contents> 227 </assert_contents>
227 </output> 228 </output>
228 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="100" /> 229 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" />
229 </test> 230 </test>
230 <!-- Other format input tests --> 231 <!-- Other format input tests -->
231 <!-- ::: Empty Drops, same as above but input is h5ad --> 232 <!-- ::: Empty Drops, same as above but input is h5ad -->
232 <test expect_num_outputs="3"> 233 <test expect_num_outputs="3">
233 <conditional name="tenx_format" > 234 <conditional name="tenx_format" >
241 <param name="use" value="emptydrops" /> 242 <param name="use" value="emptydrops" />
242 <param name="lower" value="150" /> 243 <param name="lower" value="150" />
243 <param name="fdr_thresh" value="0.02" /> 244 <param name="fdr_thresh" value="0.02" />
244 </conditional> 245 </conditional>
245 </conditional> 246 </conditional>
246 <output name="fileout_h5ad" value="defs_emptydrops_150_0002a.h5ad" compare="sim_size" delta="200" /> 247 <output name="fileout_h5ad" value="defs_emptydrops_150_0002a.h5ad" compare="sim_size" delta="400" />
247 <output name="table" > 248 <output name="table" >
248 <assert_contents> 249 <assert_contents>
249 <has_n_columns n="9" /> 250 <has_n_columns n="9" />
250 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> 251 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
251 <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" /> 252 <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
252 <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196.181449214729\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" /> 253 <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196.181449214729\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
253 </assert_contents> 254 </assert_contents>
254 </output> 255 </output>
255 <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="100" /> 256 <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="400" />
256 </test> 257 </test>
257 <!-- Output a directory --> 258 <!-- Output a directory -->
258 <test expect_num_outputs="3"> 259 <test expect_num_outputs="3">
259 <conditional name="tenx_format" > 260 <conditional name="tenx_format" >
260 <param name="use" value="tsv" /> 261 <param name="use" value="tsv" />