Mercurial > repos > bgruening > alevin
comparison alevin.xml @ 14:c9944a2600f1 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
| author | bgruening |
|---|---|
| date | Mon, 18 Mar 2024 09:36:09 +0000 |
| parents | e661a3269313 |
| children |
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| 13:e32b215b7c04 | 14:c9944a2600f1 |
|---|---|
| 1 <tool id="alevin" name="Alevin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@"> | 1 <tool id="alevin" name="Alevin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@"> |
| 2 <description>Quantification and analysis of 3-prime tagged-end single-cell sequencing data</description> | 2 <description>Quantification and analysis of 3-prime tagged-end single-cell sequencing data</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="xrefs"/> | |
| 6 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 7 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 8 mkdir ./index | 9 mkdir ./index |
| 9 && mkdir ./output | 10 && mkdir ./output |
| 10 #if $refTranscriptSource.TranscriptSource != "indexed": | 11 #if $refTranscriptSource.TranscriptSource != "indexed": |
| 267 <section name="optional"> | 268 <section name="optional"> |
| 268 <param name="keepCBFraction" value="1"/> | 269 <param name="keepCBFraction" value="1"/> |
| 269 <param name="freqThreshold" value="5"/> | 270 <param name="freqThreshold" value="5"/> |
| 270 <param name="dumpMtx" value="true"/> | 271 <param name="dumpMtx" value="true"/> |
| 271 </section> | 272 </section> |
| 272 <output name="quants_mat_mtx" file="alevin_mat_01.mtx" ftype="mtx" sort="true"/> | 273 <output name="quants_mat_mtx" file="alevin_mat_01.mtx" compare="sim_size" ftype="mtx"> |
| 274 <assert_contents> | |
| 275 <has_text text="MatrixMarket" /> | |
| 276 <has_n_columns n="5" /> | |
| 277 <has_n_lines n="105" /> | |
| 278 </assert_contents> | |
| 279 </output> | |
| 273 </test> | 280 </test> |
| 274 <test expect_num_outputs="11"> | 281 <test expect_num_outputs="11"> |
| 275 <conditional name="refTranscriptSource"> | 282 <conditional name="refTranscriptSource"> |
| 276 <param name="TranscriptSource" value="history"/> | 283 <param name="TranscriptSource" value="history"/> |
| 277 <section name="s_index"> | 284 <section name="s_index"> |
| 294 <param name="keepCBFraction" value="1"/> | 301 <param name="keepCBFraction" value="1"/> |
| 295 <param name="numCellBootstraps" value="2"/> | 302 <param name="numCellBootstraps" value="2"/> |
| 296 <param name="freqThreshold" value="5"/> | 303 <param name="freqThreshold" value="5"/> |
| 297 <param name="dumpMtx" value="true"/> | 304 <param name="dumpMtx" value="true"/> |
| 298 </section> | 305 </section> |
| 299 <output name="quants_mat_mtx" file="alevin_mat_02.mtx" ftype="mtx" sort="true"/> | 306 <output name="quants_mat_mtx" file="alevin_mat_02.mtx" compare="sim_size" ftype="mtx" > |
| 307 <assert_contents> | |
| 308 <has_text text="MatrixMarket" /> | |
| 309 <has_n_columns n="5" /> | |
| 310 <has_n_lines n="105" /> | |
| 311 </assert_contents> | |
| 312 </output> | |
| 300 </test> | 313 </test> |
| 301 <test expect_num_outputs="8"> | 314 <test expect_num_outputs="8"> |
| 302 <conditional name="refTranscriptSource"> | 315 <conditional name="refTranscriptSource"> |
| 303 <param name="TranscriptSource" value="history"/> | 316 <param name="TranscriptSource" value="history"/> |
| 304 <section name="s_index"> | 317 <section name="s_index"> |
| 321 <section name="optional"> | 334 <section name="optional"> |
| 322 <param name="keepCBFraction" value="1"/> | 335 <param name="keepCBFraction" value="1"/> |
| 323 <param name="freqThreshold" value="5"/> | 336 <param name="freqThreshold" value="5"/> |
| 324 <param name="dumpMtx" value="true"/> | 337 <param name="dumpMtx" value="true"/> |
| 325 </section> | 338 </section> |
| 326 <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" ftype="mtx" sort="true"/> | 339 <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" compare="sim_size" ftype="mtx"> |
| 340 <assert_contents> | |
| 341 <has_text text="MatrixMarket" /> | |
| 342 <has_n_columns n="5" /> | |
| 343 <has_n_lines n="105" /> | |
| 344 </assert_contents> | |
| 345 </output> | |
| 327 </test> | 346 </test> |
| 328 <test expect_num_outputs="14"> | 347 <test expect_num_outputs="14"> |
| 329 <conditional name="refTranscriptSource"> | 348 <conditional name="refTranscriptSource"> |
| 330 <param name="TranscriptSource" value="history"/> | 349 <param name="TranscriptSource" value="history"/> |
| 331 <section name="s_index"> | 350 <section name="s_index"> |
| 345 <param name="tgmap" value="minitxp.tsv"/> | 364 <param name="tgmap" value="minitxp.tsv"/> |
| 346 <param name="output_files" value="dumpFeatures,salmon_log,fragment_length,auxiliar_info,dumpUmiGraph,dumpBfh,commands"/> | 365 <param name="output_files" value="dumpFeatures,salmon_log,fragment_length,auxiliar_info,dumpUmiGraph,dumpBfh,commands"/> |
| 347 <section name="optional"> | 366 <section name="optional"> |
| 348 <param name="dumpMtx" value="true"/> | 367 <param name="dumpMtx" value="true"/> |
| 349 </section> | 368 </section> |
| 350 <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true"/> | 369 <output name="quants_mat_mtx" file="alevin_mat.mtx" compare="sim_size" ftype="mtx"> |
| 370 <assert_contents> | |
| 371 <has_text text="MatrixMarket" /> | |
| 372 <has_n_columns n="5" /> | |
| 373 <has_n_lines n="17" /> | |
| 374 </assert_contents> | |
| 375 </output> | |
| 351 <output name="salmon_quant_log" ftype="txt"> | 376 <output name="salmon_quant_log" ftype="txt"> |
| 352 <assert_contents> | 377 <assert_contents> |
| 353 <has_text text="Index contained 322 targets"/> | 378 <has_text text="Index contained 322 targets"/> |
| 354 <has_text text="Counted 14 total reads in the equivalence classes"/> | 379 <has_text text="Counted 14 total reads in the equivalence classes"/> |
| 355 </assert_contents> | 380 </assert_contents> |
| 361 </assert_contents> | 386 </assert_contents> |
| 362 </output> | 387 </output> |
| 363 <output_collection name="umigraphs" type="list" count="14"> | 388 <output_collection name="umigraphs" type="list" count="14"> |
| 364 <element name="AGTGGGATCTTAACCT"> | 389 <element name="AGTGGGATCTTAACCT"> |
| 365 <assert_contents> | 390 <assert_contents> |
| 366 <has_size value="4017" delta="1000"/> | 391 <has_size value="4661" delta="1000"/> |
| 367 </assert_contents> | 392 </assert_contents> |
| 368 </element> | 393 </element> |
| 369 </output_collection> | 394 </output_collection> |
| 370 <output name="bfh_txt" file="full_data_structure.txt" ftype="txt"/> | 395 <output name="bfh_txt" file="full_data_structure.txt" ftype="txt"/> |
| 371 </test> | 396 </test> |