| Previous changeset 9:6bf9de09aa74 (2022-04-11) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit cf30b4fab90cf7910bb2900a05b85ca3344aae59 |
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modified:
barplot.r sr_bowtie_dataset_annotation.xml |
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added:
test-data/unmatched_6.fa |
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| diff -r 6bf9de09aa74 -r fd4a60fc3fca barplot.r --- a/barplot.r Mon Apr 11 00:27:41 2022 +0000 +++ b/barplot.r Tue Nov 15 00:45:36 2022 +0000 |
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| @@ -1,13 +1,13 @@ if (length(commandArgs(TRUE)) == 0) { - system("Rscript barplot.r -h", intern = F) + system("Rscript barplot.r -h", intern = FALSE) q("no") } # load packages that are provided in the conda env -options(show.error.messages = F, +options(show.error.messages = FALSE, error = function() { cat(geterrmessage(), file = stderr()) - q("no", 1, F) + q("no", 1, FALSE) } ) loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") @@ -35,7 +35,7 @@ opt <- parse_args(OptionParser(option_list = option_list), args = commandArgs(trailingOnly = TRUE)) -annotations <- read.delim(opt$input, header = F) +annotations <- read.delim(opt$input, header = FALSE) colnames(annotations) <- c("sample", "class", "percent_of_reads", "total") annotations$percent <- round(annotations$percent_of_reads / annotations$total * 100, digits = 2) @@ -51,7 +51,7 @@ geom_bar(position = "fill", stat = "identity") + facet_wrap(~sample, ncol = 3) + geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), - size = 2, show.legend = F) + + size = 2, show.legend = FALSE) + coord_polar(theta = "y") + labs(x = "Class fractions (%)") + scale_fill_manual(values = mycolors) + |
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| diff -r 6bf9de09aa74 -r fd4a60fc3fca sr_bowtie_dataset_annotation.xml --- a/sr_bowtie_dataset_annotation.xml Mon Apr 11 00:27:41 2022 +0000 +++ b/sr_bowtie_dataset_annotation.xml Tue Nov 15 00:45:36 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.7"> +<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.8"> <description>by iterative alignments with sRbowtie</description> <requirements> <requirement type="package" version="1.3.1">bowtie</requirement> @@ -8,14 +8,14 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ #if $refGenomeSource1.genomeSource == "history": - bowtie-build -f $refGenomeSource1.ownFile genome 1>/dev/null && + bowtie-build --threads \${GALAXY_SLOTS:-4} -f $refGenomeSource1.ownFile genome 1>/dev/null && #set index_path = 'genome' #else: #set index_path = $refGenomeSource1.index.fields.path #end if #for $i in $AdditionalQueries: - bowtie-build -f $i.ownFile $i.ownFile.name 1>/dev/null && + bowtie-build --threads \${GALAXY_SLOTS:-4} -f $i.ownFile $i.ownFile.name 1>/dev/null && #end for #set method_prefix = "-v %s -k 1 --best" % str($mismatches) @@ -121,11 +121,11 @@ <output name="output" ftype="tabular" file="multisample5_output.tab" /> <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" /> <output_collection name="unmatched" type="list" count="5"> - <element name="sample5.fa_unmatched" file="unmatched_5.fa" ftype="fasta"/> - <element name="sample4.fa_unmatched" file="unmatched_4.fa" ftype="fasta"/> - <element name="sample3.fa_unmatched" file="unmatched_3.fa" ftype="fasta"/> - <element name="sample2.fa_unmatched" file="unmatched_2.fa" ftype="fasta"/> - <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/> + <element name="sample5.fa_unmatched" file="unmatched_5.fa" ftype="fasta" compare="sim_size" delta="0"/> + <element name="sample4.fa_unmatched" file="unmatched_4.fa" ftype="fasta" compare="sim_size" delta="0"/> + <element name="sample3.fa_unmatched" file="unmatched_3.fa" ftype="fasta" compare="sim_size" delta="0"/> + <element name="sample2.fa_unmatched" file="unmatched_2.fa" ftype="fasta" compare="sim_size" delta="0"/> + <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta" compare="sim_size" delta="0"/> </output_collection> </test> <test> @@ -137,7 +137,7 @@ <output name="output" ftype="tabular" file="sample1_output.tab" /> <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/> <output_collection name="unmatched" type="list"> - <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/> + <element name="sample1.fa_unmatched" file="unmatched_6.fa" ftype="fasta" compare="sim_size" delta="0"/> </output_collection> </test> <test> |
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| diff -r 6bf9de09aa74 -r fd4a60fc3fca test-data/unmatched_6.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unmatched_6.fa Tue Nov 15 00:45:36 2022 +0000 |
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| b'@@ -0,0 +1,530 @@\n+>25207\n+TCGCACTAGCTTCGGTCGTCTCGGA\n+>25229\n+TCTGTTCGAGGTTCTTTATTTGAA\n+>25283\n+TAAGGGAGCGAGATCGTTCGATGCA\n+>25363\n+TAGTGTTGGGTGTAGGCCAGGGAG\n+>25376\n+TCCGCCGACAATGTTGCAACATGA\n+>25435\n+TTTCTTCAAGCTGCGCGTTTTTCGG\n+>25593\n+TCGAAAACTTCTTCGCACTCTTCGTT\n+>25660\n+TCTCGCTGCGTGAACGATGAAGGC\n+>25968\n+TTTGCTAGGACTGCTGCATAAG\n+>26220\n+GCCCGTGTCGATGAATGCTTCAAACT\n+>26261\n+TATTATCGTCCGCTGCTAAACTGC\n+>26543\n+CTTATGTATAAAAAGCTCTGATGGA\n+>26610\n+TCCTTAAGTTCGTTGATTTGGGCT\n+>26675\n+CAATATCGTCAACATCCTCGAACGAT\n+>26873\n+TTGGGAGCTGAATCCCGTTACGGTA\n+>26978\n+CGCGCATTAGCTCAAATCTAGTTGGA\n+>27220\n+TGTTTATTTGTCAAGTTTAGATAATA\n+>27397\n+TAGTTCACAGCTGTATGTCCAGATGGGT\n+>27869\n+TATGGTCCAGAATGTAGCCTCGGC\n+>27878\n+TATTAATCGGGCCACAAATATCGGTA\n+>28035\n+GGTATTCTTTGCGAGGTCGTCCTGG\n+>28154\n+AAAGACGAGAACGCGTATATGTGTGC\n+>28319\n+TGACCAACCTTAAAAGATCGGGGT\n+>28387\n+TATTACTATTTCTAAGCTTTGTTTAAA\n+>28594\n+TTTTGAGGTTGGTCAAGAAGTTGTT\n+>28608\n+TAAGATTGAAAATTACTGTGGAGT\n+>28668\n+TACAGATTCTAGAGACAAAGACGC\n+>28674\n+TAAGTACATGCGCCCAGCCGCCGTGA\n+>28836\n+TCTGGTTAAGGTCGGAATACTCGTCT\n+>29056\n+TGCTTTACATACCCTTTGGTGCCC\n+>29323\n+TTTTGCTGCAGAGCTTCTTCCAACGT\n+>29342\n+TATGTATGGATATGTATATTTATGGT\n+>29387\n+TGATAATCGACCTCTTCCATCGTTGT\n+>29423\n+TCTAAGAACTTCTGAGGTGAAGG\n+>29462\n+TGCATTTCAATCGGAAGAGTACTCTG\n+>29492\n+TAAAACACAAATCTCGACATACAGA\n+>29703\n+GTACAGGTTCTGATGACAATG\n+>29785\n+TCAGATGAAAGACAAATTAGAATT\n+>30053\n+TAAGAACTTCTGAGATGAAGGGC\n+>30096\n+TGGATATTGAATGTTTTTGATTTGC\n+>30136\n+TGTAGTCGTCGTATGTCCGGA\n+>30272\n+TGCATTCGTGGATTCGCATTCGAGA\n+>30497\n+TGACAAAATATGCCCTTCACCTCAGA\n+>30787\n+TAACTGTTTTTAGTTCAAAGTCTCGGA\n+>30836\n+TAAATATTTTTTTTGAAACA\n+>30977\n+CGACTGTAATTATTAGCACAATACT\n+>30985\n+GACGATATTGCTGCAATAGACCTTGA\n+>31000\n+TCAGATGAGAGACAAATTAGAAT\n+>31256\n+TAATTCGGAATGCCTGCTCTACT\n+>31417\n+TCAATGATCGCTGTGCTCAGTAGGA\n+>31506\n+TTTGTCTGACGTTAAAAAATATA\n+>31567\n+TCCACATTAGGAGGATTATTAGACAAC\n+>31790\n+AAACATAATAATTGATGGCGGAAGA\n+>31872\n+AAGGTAATCATAGAGCACCACGGTT\n+>32157\n+TTTCTGTGAATTCACATGCTGATGA\n+>32192\n+TTTCTCATGTATAAAATGCTCTGATGG\n+>32223\n+TATCTTGTTATTCTAGTGTCTTTGGTT\n+>32338\n+TGTGGGACTCGAGCCAAAATGGCAACCT\n+>32497\n+TGCGGTTGGACAATTTTTTTTTTATA\n+>32506\n+TTGTTGTTTGGAGGAAGTTCCTTT\n+>32510\n+TCTTCCGCCATCAATTATTATGTTTT\n+>32522\n+TACTTGACTTTTCTATAGAATCTGGT\n+>32540\n+TATCGTCAACATCCTCGAACGATCGAGA\n+>32626\n+TTGATCAAGGTAGGGTTGTCGC\n+>32646\n+TCTGTTAAACACCCCTGAATCGTGGAT\n+>32657\n+TTTGGACATTTTGCAGGTGATACAAT\n+>32682\n+TAACTGTTTTTAGTTCAAAGTCTCGGA\n+>32716\n+TATCTATAGTTCCGATTGGCCATCTC\n+>32885\n+GAAAGTGGGTATCTGTATTTTAGGC\n+>32967\n+TAAAGATACCATCTAACCTCCTTGGA\n+>33075\n+ACAGATATTAGTGTTTTTCAAGCAGC\n+>33147\n+ATCGCAATTATGGCATAACAGATTCGGA\n+>33163\n+TTCAGCGTCGCTTGATTGAATAGAT\n+>33231\n+TAAGAACTTCTGAGGTGAAGGGC\n+>33242\n+TTGGGTTTAGAAATTAAAATTAAGGC\n+>33244\n+TATAGAAAGTTACGAATATATTAGGA\n+>33248\n+TTTTTGATCAATTGGCACCGTGCGAA\n+>33296\n+TGCAGAGCTTCTTCCAACGTTGGCAAG\n+>33318\n+TAGATGTCTGCAGGAATAACGGA\n+>33338\n+TCGACTATTAATGGCTGTTAGAATT\n+>33475\n+CAAACTTATCGACCATCTCCTCAAACG\n+>33601\n+TTACCCTTTTTCCGGAGCGTTTGTGC\n+>33611\n+AATGATCGCTGTGCTCAGTATGACGG\n+>33662\n+TTTGATTCATTACAATTTACGCTGAA\n+>33737\n+CAGATATTAGTGTTTTTCAAGCAGC\n+>33747\n+TACATGTAAAGCAGCTGTGTGTGC\n+>33815\n+AGTTTTTGGAATCACTTGA\n+>34032\n+TGCGGACGTGTGCTCGCTGCGTGA\n+>34200\n+TAATATATGTATAATCTGCTTGGTG\n+>34240\n+TCTTTACGCCATATAAATCATTTCGA\n+>34259\n+ACAAATCATAAATTTGATGGGACGA\n+>34268\n+TCTTGTGGACTTCACTCTAG\n+>34297\n+TAAGTAAATAGTCCCCGCCTTATTGAGG\n+>34337\n+TGGATAATGAATGTTTTTGATTTGC\n+>34569\n+TCTAGGTTCTTCTGAAATCGTGGGA\n+>34643\n+TCGTGTAGACCGGATAAGATTTTTT\n+>34697\n+TCTAATACTGTGAAAGGGTGGGG\n+>34808\n+GTAGGATGTGCTCTGCGGTTTCCAC\n+>34892\n+TCTGTCGCAGTTGTAGCTTGCAATA\n+>34896\n+TGTAGTTGCCACTTATGCTGTCCA\n+>35151\n+TAGCAATGTCCGTCTGTCCGTATGA\n+>35196\n+TGTAAATGGTCAGCGAAAGCAAAGG\n+>35211\n+CAGATATTAGTGTTTTTCAAGCAGCGG\n+>35246\n+CCTCAGAGAACGTCAGACCGCG\n+>35272\n+TGCAGAGCTTCTTCCAACGTTGG\n+>35273\n+TCTGGTAGTAAGAAAAATGTAGCTT\n+>35286\n+TATGTATGGATATGTATATTTATGGGT\n+>35317\n+TTTTGGTTTGATCGTCAGGTGGTC\n+>35512\n+GACGATAATAGTGAATTTTGGACA\n+>35566\n+TTCGAATTCGCGCCATTTCACAATC\n+>35948\n+TGGCCTGTATACGCTTTCTGTTG\n+>36009\n+TTGCAAAAGTCATATCTTGAGG\n+>36059\n+TAAGTTACTATGGATCCATAAGGGTA\n+>36100\n+TGATATGGGACTTGTAGCTTTTTT'..b'54\n+TAATAGTCAGGGCGCGAATTTTTAAAA\n+>39325\n+TTAGGACTTATTGAACTTTACGGTA\n+>39359\n+TATGCAAATCAAGTGTGACCGTAGCT\n+>39450\n+TTAAACAACGATATAGTGGACAGTA\n+>39453\n+TCTGCCGGATTTTGATCCAATCAAGG\n+>39819\n+GTGGAATTGAAAAAGAACCAGACACA\n+>40040\n+TTTTTGGAACTACCTGAGTCGGTT\n+>40183\n+TAACACAAAGCAGTATGATTTAATAAT\n+>40189\n+CAGCAAGCTGAGATGTACATTAGTATA\n+>40374\n+TACGTTTTCTTGCAGATCAAAAA\n+>40445\n+CGTTCTTTAAAACCACCAATGGGA\n+>40467\n+TACGCAGATTCCTGGGAGTTACAGGA\n+>40488\n+TGATTTGGGCTTGCATACTTGTACT\n+>40797\n+TATATTCGTGTTCATGTGTGAACAGC\n+>40831\n+TCTAAGAACTTCTGAGGTGAAGGGC\n+>40951\n+TTCTTCGTAAGTCAAAATAGTGTCGCC\n+>40988\n+TATGATTGATTGCTTGAGAGT\n+>40998\n+TGATAGAGCTGCATTTGAATTAACGG\n+>41061\n+CTCTTTCCGCTCACTCCCGCTGAGA\n+>41076\n+TGCATTAAGAAGATTTAGGATCC\n+>41140\n+TCAAGGATTAATGTAGGGGGGG\n+>41143\n+CAATAGCGTCGCTGAGTAACAGTG\n+>41162\n+TACGGATTGCAGCGGCTAG\n+>41183\n+TTTTTTGGCACACGATTTTTTGGACGT\n+>41227\n+TAATATATGTATACTCTGCTTGGTG\n+>41265\n+TTTATGATTTTTGGTAATA\n+>41365\n+TAGGAGGGTTCCACAACTATTTCGGGG\n+>41837\n+TAGTTTGACACTGTTTGGAGACGTGG\n+>42053\n+TCTGTGGTCGAATCGAAGGAGTGC\n+>42113\n+TAATAGATCGCTCACCTGTTCCTGG\n+>42392\n+CGGCATCGGAAAACTCCCAGCGGGGC\n+>42504\n+TAACGTTATTATTATTTGAAAATAGAA\n+>42566\n+TTTGTTGGGTAGGAACTTTACTGC\n+>42668\n+TGCTGCAGAGCTTCTTCCAACGTTGG\n+>42751\n+CCAAAGTCTGGTTGTCAGAAAATGTGC\n+>42777\n+AAGGAAGGAACCAAAGAAGCACAAACG\n+>42804\n+TAATTCTAATTTGTCTCTCATCTGA\n+>42830\n+TAGTATACTTATTAAGTCATTTGA\n+>42857\n+AGAGTATTCATCTTGAGGCGTGTG\n+>42886\n+TGAACAACGATTTATGTATATAAGAA\n+>42899\n+TACGATAATAGTGAATTTTGGACA\n+>42936\n+TTTGACTAAAAGTCGCTTGTTTTGGA\n+>43050\n+AATACATAACTCTGGACACAGGAGA\n+>43219\n+TACTTTCGTCAAAATGTTCAGGAGCT\n+>43242\n+TGACATGTCTATTTCCATGGGTTCGGA\n+>43268\n+GTGTATAAAAAAATTTATTGTTGAGCA\n+>43299\n+TCTGGATGATGGCTGATGCTCGTTG\n+>43491\n+TCTGATGACAATGAATTTTTTAGACA\n+>43520\n+TATTGTTGTAATTGCTGCCTCGGTTG\n+>43654\n+ATATGAACAAAGCAAAGACACTAGAA\n+>43677\n+CACGATTCATAACCCTCAGCTGAAG\n+>43776\n+GCTCCTGGCAACTCTGTGATGGAC\n+>43903\n+TATTTTGATGTTTAATGAA\n+>43990\n+TTTCTACTTCGTATTATTTTTATGA\n+>44062\n+AAACATAATAATTGATGGCGGAAGA\n+>44071\n+CACAGACGCAGTGGAAACCGCAGA\n+>44078\n+CGTGCGTCCGAGCAAAAGGTGGT\n+>44187\n+TTATGTAAGAATATTTGTCATTAGA\n+>44239\n+TATCAATGTTGACCGTAATACTCAA\n+>44253\n+TGGATATTGAATGTTTTTGATTTGC\n+>44279\n+TGTGATTTTCCCAATTTATATTAATACA\n+>44374\n+TAGTCGGAGTTGATGAGCTGCC\n+>44412\n+TCCGAATTTTCTGTCGCAGTTGTAGCT\n+>44423\n+TCGGCTTGGGTTTAGAAATTAAAAT\n+>44558\n+ACAAATCATAAATTTGGTGGGA\n+>44637\n+TTTTTTATCAATTGGCACCATGCGAA\n+>44642\n+TACTGTGTGCTGGCCTTGATGAAAGT\n+>44688\n+TAGATGTCTGCACGAATAACGGA\n+>44945\n+TGCTTCCGAGCAATCTACGTTGGTAAAA\n+>45054\n+TCTCATCTGACAATTTTTTAAAAGCGA\n+>45088\n+TCTGAAGCAGCGCTCACGGCAGAATGC\n+>45203\n+TGCCGGATTTTGATCCAATCAAGGGA\n+>45263\n+TATTGATTTTCCTATTTAGTTGAACA\n+>45274\n+AAAAGTCTGGATATTGTAGGATAGGA\n+>45358\n+CAACGCTGGACCTTGGACTCGAGGGC\n+>45396\n+CATCTTGTTATTCTAGTGTCTTTGGTA\n+>45641\n+GAACTAAGATCAGTCGACTGTAATTAT\n+>45774\n+CGACGAACTAGCAGCTCTGGTGT\n+>45911\n+CAGATATTAGTGTTTTTCAAGCAGC\n+>45997\n+TTAACCAGTCGGCGTTGTTTAAGTAGC\n+>46031\n+AAAGCGTCTACTTGAACAATGAGA\n+>46054\n+TTAGATCGTATTACTTGGGTGCTGG\n+>46199\n+TAAGCGTTAGGTCGTATTACTTGGGC\n+>46255\n+TAAGATTGAAAATTACTGTGGAGTAAT\n+>46366\n+TAAGGAATTGTCGGCCATTTAATGTGA\n+>46387\n+CAGAGCTTCTTCCAACGTTGGCAAG\n+>46701\n+TTGTATCTTTTTGCTTTTTATATT\n+>46705\n+TAACTGTTTTTAGTTCAAAGTCTCGGA\n+>46783\n+TCTCATCTGACAATTTTTTAAAAGCGA\n+>46836\n+TCATAAGGACAGACGGACAT\n+>46892\n+AAACATAATAATTGATGGCGGAAGA\n+>47244\n+TCTCTGTCCGCTCGCTTACGATGAGA\n+>47290\n+TTTCAGGAATGGGGTCGTCCCACTA\n+>47348\n+TGCAAAAGTAATATCAAAGACACTA\n+>47359\n+TTTAAAATTATAATAGTCAGGG\n+>47427\n+CATCTTGTTATTCTAGTGTCTTTGGT\n+>47654\n+TTAAACACTGAATTCGGTTTCGAAA\n+>47656\n+TTTCTGAAGAATCCTGTAACTCCC\n+>47785\n+TGTAGATGAGCGGCAAATGTGG\n+>47827\n+TTGATCAAGGTAGAGTTGTCGCGC\n+>48184\n+TTCAAGGATTAATGTAGGGGGGG\n+>48576\n+TTAACCCGGAGACTTGGGTGTGGGT\n+>48764\n+TGCAAAAGTAATATCAAAGACAATAGA\n+>48782\n+TGACAATGTAGTGAACGCCAGTGT\n+>48893\n+TATAAATGCCGTCTGATATTATTAAA\n+>49017\n+ACCGGATGTCATATCCAGCGTCGTGAA\n+>49381\n+TACAATGTAAATTCGTTTCTTCGATCA\n+>49456\n+TTTTGGTTTGATCGTCAGGTGGACGC\n+>49484\n+TCTGCTATCATTGACTCGATCATTGA\n+>49569\n+TCGATTGTATGATCAGTGGAAGTGGC\n+>49602\n+GAAATTGGCCAACATTAATTCGGAA\n+>49628\n+TACTTTCGTCAAAATGTTCAGGAGC\n+>49715\n+TTTGTCCGGGTGCTTCGAAAGAACTCT\n+>49778\n+CAATAGCGTCGCTGAGTAACAGTG\n' 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