Mercurial > repos > iuc > rna_starsolo
comparison rg_rnaStarSolo.xml @ 17:5ef7ec16b04f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
author | iuc |
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date | Fri, 01 Sep 2023 13:18:03 +0000 |
parents | b8f5f6e87f5c |
children |
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16:13022c3d3076 | 17:5ef7ec16b04f |
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1304 <has_line_matching expression="ENSG00000275464\s+38\s+1\s+40" /> | 1304 <has_line_matching expression="ENSG00000275464\s+38\s+1\s+40" /> |
1305 </assert_contents> | 1305 </assert_contents> |
1306 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> | 1306 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> |
1307 </output> | 1307 </output> |
1308 </test> | 1308 </test> |
1309 <test expect_num_outputs="6"> | |
1310 <!-- test 13 | |
1311 If the splice feature set is not set correctly, | |
1312 "Fatal INPUT FILE error, no exon lines in the GTF file" is expected --> | |
1313 <conditional name="refGenomeSource"> | |
1314 <param name="geneSource" value="history" /> | |
1315 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> | |
1316 <param name="genomeSAindexNbases" value="4" /> | |
1317 <param name="sjdbOverhang" value="100" /> | |
1318 <param name="sjdbGTFfile" value="fakexon.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/> | |
1319 <param name="sjdbGTFfeatureExon" value="fakexon"/> | |
1320 </conditional> | |
1321 <conditional name="sc" > | |
1322 <param name="solo_type" value="CB_UMI_Simple" /> | |
1323 <conditional name="input_types"> | |
1324 <param name="use" value="repeat" /> | |
1325 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" /> | |
1326 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" /> | |
1327 </conditional> | |
1328 <param name="soloCBwhitelist" value="filtered.barcodes.txt" /> | |
1329 <conditional name="params"> | |
1330 <param name="chemistry" value="Cv3" /> | |
1331 </conditional> | |
1332 <conditional name="umidedup"> | |
1333 <param name="soloUMIdedup" value="1MM_All" /> | |
1334 </conditional> | |
1335 </conditional> | |
1336 <section name="solo" > | |
1337 <conditional name="filter"> | |
1338 <param name="filter_type" value="no_filter" /> | |
1339 </conditional> | |
1340 <param name="soloStrand" value="Forward" /> | |
1341 <param name="soloFeatures" value="Gene Velocyto" /> | |
1342 <param name="quantModeGene" value="true" /> | |
1343 </section> | |
1344 <output name="output_barcodes" > | |
1345 <assert_contents> | |
1346 <!-- first and last line --> | |
1347 <has_line line="AAACCTGAGCGCTCCA" /> | |
1348 <has_line line="TTTGGTTAGTGGGCTA" /> | |
1349 <has_n_lines n="394" /> | |
1350 </assert_contents> | |
1351 </output> | |
1352 <output name="output_genes"> | |
1353 <assert_contents> | |
1354 <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" /> | |
1355 <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" /> | |
1356 <has_n_lines n="14" /> | |
1357 </assert_contents> | |
1358 </output> | |
1359 <output name="output_stats" > | |
1360 <assert_contents> | |
1361 <has_line_matching expression="\s+noUnmapped\s+0" /> | |
1362 <has_line_matching expression="\s+yesUMIs\s+36" /> | |
1363 </assert_contents> | |
1364 </output> | |
1365 <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" /> | |
1366 <output name="reads_per_gene" > | |
1367 <assert_contents> | |
1368 <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" /> | |
1369 <has_line_matching expression="ENSG00000275464\s+38\s+1\s+40" /> | |
1370 </assert_contents> | |
1371 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> | |
1372 </output> | |
1373 </test> | |
1309 </tests> | 1374 </tests> |
1310 <help><![CDATA[ | 1375 <help><![CDATA[ |
1311 **What it does** | 1376 **What it does** |
1312 | 1377 |
1313 **STARSolo** is a turnkey solution for analyzing droplet single cell RNA sequencing data (e.g. 10X Genomics Chromium System) built directly into STAR_ code. STARsolo takes raw FASTQ reads files as input, and performs the following operations: | 1378 **STARSolo** is a turnkey solution for analyzing droplet single cell RNA sequencing data (e.g. 10X Genomics Chromium System) built directly into STAR_ code. STARsolo takes raw FASTQ reads files as input, and performs the following operations: |