Mercurial > repos > iuc > dropletutils
comparison dropletutils.xml @ 6:8855361fcfc5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
author | iuc |
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date | Thu, 10 Dec 2020 13:50:06 +0000 |
parents | cdf4443d5625 |
children | 2c1200fba922 |
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5:cdf4443d5625 | 6:8855361fcfc5 |
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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="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > |
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 <xrefs> | |
5 <xref type="bio.tools">dropletutils</xref> | |
6 </xrefs> | |
7 <edam_topics> | |
8 <edam_topic>topic_0203</edam_topic> | |
9 <edam_topic>topic_3168</edam_topic> | |
10 <edam_topic>topic_3170</edam_topic> | |
11 <edam_topic>topic_3308</edam_topic> | |
12 </edam_topics> | |
13 <edam_operations> | |
14 <edam_operation>operation_1812</edam_operation> | |
15 <edam_operation>operation_3200</edam_operation> | |
16 </edam_operations> | |
4 <macros> | 17 <macros> |
5 <token name="@PACKAGE_VERSION@" >1.2.1</token> | 18 <token name="@TOOL_VERSION@">1.10.0</token> |
6 <token name="@GALAXY_VERSION@" >galaxy6</token> | 19 <token name="@VERSION_SUFFIX@">0</token> |
7 <token name="@TXIN@">tenx.input</token> | 20 <token name="@TXIN@">tenx.input</token> |
8 <token name="@TXOUT@">tenx.output</token> | 21 <token name="@TXOUT@">tenx.output</token> |
9 <xml name="test_dirin" > | 22 <xml name="test_dirin" > |
10 <conditional name="tenx_format"> | 23 <conditional name="tenx_format"> |
11 <param name="use" value="directory" /> | 24 <param name="use" value="directory" /> |
14 <param name="input_genes" value="in_genes.tsv" /> | 27 <param name="input_genes" value="in_genes.tsv" /> |
15 </conditional> | 28 </conditional> |
16 </xml> | 29 </xml> |
17 </macros> | 30 </macros> |
18 <requirements> | 31 <requirements> |
19 <requirement type="package" version="@PACKAGE_VERSION@">bioconductor-dropletutils</requirement> | 32 <requirement type="package" version="@TOOL_VERSION@">bioconductor-dropletutils</requirement> |
20 <requirement type="package" version="1.2_17" >r-matrix</requirement> | 33 <requirement type="package" version="1.18.0" >bioconductor-scater</requirement> |
21 <requirement type="package" version="1.10.1" >bioconductor-scater</requirement> | 34 <requirement type="package" version="4.0">r-base</requirement> |
35 <requirement type="package" version="1.2_18">r-matrix</requirement> | |
22 <requirement type="package" version="1">fonts-conda-ecosystem</requirement> | 36 <requirement type="package" version="1">fonts-conda-ecosystem</requirement> |
23 </requirements> | 37 </requirements> |
24 <version_command><![CDATA[ | 38 <version_command><![CDATA[ |
25 Rscript -e 'packageVersion("DropletUtils")' | grep -oP '\d\.\d\.\d' | 39 Rscript -e 'packageVersion("DropletUtils")' | grep -oP '\d\.\d\.\d' |
26 ]]> | 40 ]]> |
43 ]]> | 57 ]]> |
44 </command> | 58 </command> |
45 <configfiles> | 59 <configfiles> |
46 <configfile name="droplet_conf" > | 60 <configfile name="droplet_conf" > |
47 ## defaults | 61 ## defaults |
48 empty.fdr_threshold = 0.01 | 62 empty_fdr_threshold = 0.01 |
49 eparams=formals(emptyDrops) | 63 eparams = formals(emptyDrops) |
50 dparams=formals(defaultDrops) | 64 dparams = formals(defaultDrops) |
51 bparams=formals(barcodeRanks) | 65 bparams = formals(barcodeRanks) |
52 | 66 |
53 ## File params | 67 ## File params |
54 in.type='$tenx_format.use' | 68 intype='$tenx_format.use' |
55 out.type=NULL | 69 outtype=NULL |
56 | 70 |
57 files=list() | 71 files=list() |
58 files\$table='$table' | 72 files\$table='$table' |
59 files\$plot='$plot' | 73 files\$plot='$plot' |
60 files\$out=NULL | 74 files\$out=NULL |
72 dparams\$upper.quant=as.numeric('$operation.method.upperquant') | 86 dparams\$upper.quant=as.numeric('$operation.method.upperquant') |
73 dparams\$lower.prop=as.numeric('$operation.method.lowerprop') | 87 dparams\$lower.prop=as.numeric('$operation.method.lowerprop') |
74 #else if str($operation.method.use) == 'emptydrops': | 88 #else if str($operation.method.use) == 'emptydrops': |
75 do.method="emptyDrops" | 89 do.method="emptyDrops" |
76 eparams\$lower=as.integer('$operation.method.lower') | 90 eparams\$lower=as.integer('$operation.method.lower') |
77 empty.fdr_threshold=as.numeric('$operation.method.fdr_thresh') | 91 empty_fdr_threshold=as.numeric('$operation.method.fdr_thresh') |
78 #end if | 92 #end if |
79 | 93 |
80 out.type='$operation.outformat' | 94 outtype='$operation.outformat' |
81 #if str($operation.outformat) == 'directory': | 95 #if str($operation.outformat) == 'directory': |
82 files\$out='@TXOUT@' | 96 files\$out='@TXOUT@' |
83 #else if str($operation.outformat) == 'h5': | 97 #else if str($operation.outformat) == 'h5': |
84 files\$out='$fileout_h5' | 98 files\$out='$fileout_h5' |
85 #else if str($operation.outformat) == 'tsv': | 99 #else if str($operation.outformat) == 'tsv': |
170 <filter>operation['use']=='filter' and operation['method']['use']=="emptydrops"</filter> | 184 <filter>operation['use']=='filter' and operation['method']['use']=="emptydrops"</filter> |
171 </data> | 185 </data> |
172 </outputs> | 186 </outputs> |
173 <tests> | 187 <tests> |
174 <!-- Directory input tests --> | 188 <!-- Directory input tests --> |
175 <!-- ::: Default Drops --> | |
176 <test expect_num_outputs="1"> | 189 <test expect_num_outputs="1"> |
190 <!-- ::: Default Drops --> | |
177 <expand macro="test_dirin" /> | 191 <expand macro="test_dirin" /> |
178 <conditional name="operation"> | 192 <conditional name="operation"> |
179 <param name="use" value="filter" /> | 193 <param name="use" value="filter" /> |
180 <param name="outformat" value="h5" /><!-- H5 --> | 194 <param name="outformat" value="h5" /><!-- H5 --> |
181 </conditional> | 195 </conditional> |
194 <has_text_matching expression="GENE50\s4\s0\s0\s0\s0\s5\s11\s8\s5" /> | 208 <has_text_matching expression="GENE50\s4\s0\s0\s0\s0\s5\s11\s8\s5" /> |
195 <has_text_matching expression="GENE100\s6\s3\s5\s0\s0\s16\s31\s15\s26" /> | 209 <has_text_matching expression="GENE100\s6\s3\s5\s0\s0\s16\s31\s15\s26" /> |
196 </assert_contents> | 210 </assert_contents> |
197 </output> | 211 </output> |
198 </test> | 212 </test> |
199 <!-- :: Barcode Ranks --> | |
200 <test expect_num_outputs="1"> | 213 <test expect_num_outputs="1"> |
214 <!-- :: Barcode Ranks --> | |
201 <expand macro="test_dirin" /> | 215 <expand macro="test_dirin" /> |
202 <conditional name="operation"> | 216 <conditional name="operation"> |
203 <param name="use" value="barcode_rank" /> | 217 <param name="use" value="barcode_rank" /> |
204 <param name="lower" value="120" /> | 218 <param name="lower" value="120" /> |
205 </conditional> | 219 </conditional> |
206 <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="400"/> | 220 <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="600"/> |
207 </test> | 221 </test> |
208 <!-- ::: Empty Drops --> | |
209 <test expect_num_outputs="3"> | 222 <test expect_num_outputs="3"> |
223 <!-- ::: Empty Drops --> | |
210 <expand macro="test_dirin" /> | 224 <expand macro="test_dirin" /> |
211 <conditional name="operation"> | 225 <conditional name="operation"> |
212 <param name="use" value="filter" /> | 226 <param name="use" value="filter" /> |
213 <param name="outformat" value="h5" /> | 227 <param name="outformat" value="h5" /> |
214 <conditional name="method"> | 228 <conditional name="method"> |
219 </conditional> | 233 </conditional> |
220 <output name="fileout_h5" value="defs_emptydrops_150_0002.h5" compare="sim_size" delta="10" /> | 234 <output name="fileout_h5" value="defs_emptydrops_150_0002.h5" compare="sim_size" delta="10" /> |
221 <output name="table" > | 235 <output name="table" > |
222 <assert_contents> | 236 <assert_contents> |
223 <has_n_columns n="9" /> | 237 <has_n_columns n="9" /> |
224 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> | 238 <has_line_matching expression="^\sbar_names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis_cell\sis_cellandlimited" /> |
225 <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" /> | 239 <has_line_matching expression="^994\sGGCATTACAA\s338\s-246\.(.*TRUE){3}$" /> |
226 <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166.644236503983\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" /> | 240 <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166\.(.*TRUE){3}$" /> |
227 </assert_contents> | 241 </assert_contents> |
228 </output> | 242 </output> |
229 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" /> | 243 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" /> |
230 </test> | 244 </test> |
231 <!-- Other format input tests --> | 245 <!-- Other format input tests --> |
232 <!-- ::: Empty Drops, same as above but input is h5 --> | |
233 <test expect_num_outputs="3"> | 246 <test expect_num_outputs="3"> |
247 <!-- ::: Empty Drops, same as above but input is h5 --> | |
234 <conditional name="tenx_format" > | 248 <conditional name="tenx_format" > |
235 <param name="use" value="h5" /> | 249 <param name="use" value="h5" /> |
236 <param name="input" value="in_matrix.h5" /> | 250 <param name="input" value="in_matrix.h5" /> |
237 </conditional> | 251 </conditional> |
238 <conditional name="operation"> | 252 <conditional name="operation"> |
246 </conditional> | 260 </conditional> |
247 <output name="fileout_h5" value="defs_emptydrops_150_0002a.h5" compare="sim_size" delta="400" /> | 261 <output name="fileout_h5" value="defs_emptydrops_150_0002a.h5" compare="sim_size" delta="400" /> |
248 <output name="table" > | 262 <output name="table" > |
249 <assert_contents> | 263 <assert_contents> |
250 <has_n_columns n="9" /> | 264 <has_n_columns n="9" /> |
251 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> | 265 <has_line_matching expression="^\sbar_names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis_cell\sis_cellandlimited" /> |
252 <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" /> | 266 <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198\.(.*TRUE){3}$" /> |
253 <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196.181449214729\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" /> | 267 <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196\.(.*TRUE){3}$" /> |
254 </assert_contents> | 268 </assert_contents> |
255 </output> | 269 </output> |
256 <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="400" /> | 270 <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="400" /> |
257 </test> | 271 </test> |
258 <!-- Output a directory --> | 272 <!-- Output a directory --> |