Mercurial > repos > q2d2 > qiime2__cutadapt__trim_paired
changeset 1:4f340404bbf8 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732
| author | q2d2 |
|---|---|
| date | Fri, 13 Jan 2023 22:41:40 +0000 |
| parents | a3eb5e92ffb3 |
| children | b7fc07bacdb2 |
| files | qiime2__cutadapt__trim_paired.xml test-data/.gitkeep test-data/demux_paired.test0.md.tsv test-data/demux_paired.test0.seqs.qza test-data/demux_single.test0.md.tsv test-data/demux_single.test0.seqs.qza |
| diffstat | 5 files changed, 99 insertions(+), 6 deletions(-) [+] |
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--- a/qiime2__cutadapt__trim_paired.xml Mon Aug 29 19:21:23 2022 +0000 +++ b/qiime2__cutadapt__trim_paired.xml Fri Jan 13 22:41:40 2023 +0000 @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2022, QIIME 2 development team. +Copyright (c) 2023, QIIME 2 development team. Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> <!-- This tool was automatically generated by: - q2galaxy (version: 2022.8.1) + q2galaxy (version: 2022.11.1) for: - qiime2 (version: 2022.8.1) + qiime2 (version: 2022.11.1) --> -<tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> <description>Find and remove adapters in demultiplexed paired-end sequences.</description> <requirements> - <container type="docker">quay.io/qiime2/core:2022.8</container> + <container type="docker">quay.io/qiime2/core:2022.11</container> </requirements> <version_command>q2galaxy version cutadapt</version_command> - <command detect_errors="aggressive">q2galaxy run cutadapt trim_paired '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run cutadapt trim_paired '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -85,6 +85,11 @@ <param name="match_adapter_wildcards" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="match_adapter_wildcards: Bool" help="[default: Yes] Interpret IUPAC wildcards (e.g., N) in adapters."/> <param name="minimum_length" type="integer" min="1" value="1" label="minimum_length: Int % Range(1, None)" help="[default: 1] Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records."/> <param name="discard_untrimmed" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="discard_untrimmed: Bool" help="[default: No] Discard reads in which no adapter was found."/> + <param name="max_expected_errors" type="float" min="0" optional="true" label="max_expected_errors: Float % Range(0, None)" help="[optional] Discard reads that exceed maximum expected erroneous nucleotides."/> + <param name="max_n" type="float" min="0" optional="true" label="max_n: Float % Range(0, None)" help="[optional] Discard reads with more than COUNT N bases. If COUNT_or_FRACTION is a number between 0 and 1, it is interpreted as a fraction of the read length."/> + <param name="quality_cutoff_5end" type="integer" min="0" value="0" label="quality_cutoff_5end: Int % Range(0, None)" help="[default: 0] Trim nucleotides with Phred score quality lower than threshold from 5 prime end."/> + <param name="quality_cutoff_3end" type="integer" min="0" value="0" label="quality_cutoff_3end: Int % Range(0, None)" help="[default: 0] Trim nucleotides with Phred score quality lower than threshold from 3 prime end."/> + <param name="quality_base" type="integer" min="0" value="33" label="quality_base: Int % Range(0, None)" help="[default: 33] How the Phred score is encoded (33 or 64)."/> </section> </inputs> <outputs>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demux_paired.test0.md.tsv Fri Jan 13 22:41:40 2023 +0000 @@ -0,0 +1,77 @@ +sample-id barcode-sequence elevation extract-concen amplicon-concentration extract-group-no transect-name site-name depth ph toc ec average-soil-relative-humidity relative-humidity-soil-high relative-humidity-soil-low percent-relative-humidity-soil-100 average-soil-temperature temperature-soil-high temperature-soil-low vegetation percentcover +#q2:types categorical numeric numeric numeric categorical categorical categorical numeric numeric numeric numeric numeric numeric numeric numeric numeric numeric numeric categorical numeric +BAQ1370.1.2 GCCCAAGTTCAC 1370 0.019 0.95 B Baquedano BAQ1370 2 7.98 525 6.08 16.17 23.97 11.42 0 22.61 35.21 12.46 no 0 +BAQ1370.3 GCGCCGAATCTT 1370 0.124 17.46 E Baquedano BAQ1370 2 771 6.08 16.17 23.97 11.42 0 22.61 35.21 12.46 no 0 +BAQ1370.1.3 ATAAAGAGGAGG 1370 1.2 0.96 J Baquedano BAQ1370 3 8.13 16.17 23.97 11.42 0 22.61 35.21 12.46 no 0 +BAQ1552.1.1 ATCCCAGCATGC 1552 0.722 18.83 J Baquedano BAQ1552 1 7.87 15.75 35.36 11.1 0 22.63 30.65 10.96 no 0 +BAQ1552.2 GCTTCCAGACAA 1552 0.017 2 B Baquedano BAQ1552 2 223 1.839 15.75 35.36 11.1 0 22.63 30.65 10.96 no 0 +BAQ2420.1.1 ACACAGTCCTGA 2420 0.35 7.4 H Baquedano BAQ2420 1 9.33 82.54 100 41.135 46.77 22.45 28.297 13.294 no 0 +BAQ2420.1.2 ATTATACGGCGC 2420 0.108 11.42 H Baquedano BAQ2420 2 9.36 166 0.075 82.54 100 41.135 46.77 22.45 28.297 13.294 no 0 +BAQ2420.2 TAAACGCGACTC 2420 0.089 10.06 A Baquedano BAQ2420 2 9.36 337 0.075 82.54 100 41.135 46.77 22.45 28.297 13.294 no 0 +BAQ2420.3 CCTCGGGTACTA 2420 0.083 15.92 C Baquedano BAQ2420 2 9.36 574 0.075 82.54 100 41.135 46.77 22.45 28.297 13.294 no 0 +BAQ2420.1.3 ATTCAGATGGCA 2420 0.132 10 H Baquedano BAQ2420 3 8.9 82.54 100 41.135 46.77 22.45 28.297 13.294 no 0 +BAQ2462.1 TTCACCTGTATC 2462 1.166 15.29 H Baquedano BAQ2462 2 8.35 173 0.506 69.08 98.396 32.558 0.21 21.83 29.024 12.971 no 0 +BAQ2462.2 CTCCAGGTCATG 2462 0.049 10.39 H Baquedano BAQ2462 2 8.35 331 0.506 69.08 98.396 32.558 0.21 21.83 29.024 12.971 no 0 +BAQ2462.3 CAGGATTCGTAC 2462 0.066 8.46 A Baquedano BAQ2462 2 8.35 634 0.506 69.08 98.396 32.558 0.21 21.83 29.024 12.971 no 0 +BAQ2687.1 GTGGCCTACTAC 2687 1.223 1.24 A Baquedano BAQ2687 2 8.35 554 0.131 73.21 100 20.87 43.48 18.2 25 10.67 yes 0.1 +BAQ2687.2 TTCCCTTCTCCG 2687 0.251 17.53 C Baquedano BAQ2687 2 8.35 350 0.131 73.21 100 20.87 43.48 18.2 25 10.67 yes 0.1 +BAQ2687.3 CATTTGACGACG 2687 1.176 12.1 E Baquedano BAQ2687 2 8.35 400 0.131 73.21 100 20.87 43.48 18.2 25 10.67 yes 0.1 +BAQ2838.1 CGCATACGACCT 2838 0.467 10.91 G Baquedano BAQ2838 2 8.36 353 0.212 44.74 100 16.647 11.34 19.08 24.995 10.709 no 0 +BAQ2838.2 GCCTCGTACTGA 2838 0.309 14.38 H Baquedano BAQ2838 2 8.36 260 0.212 44.74 100 16.647 11.34 19.08 24.995 10.709 no 0 +BAQ2838.3 ACCAACAGATTG 2838 0.145 14.06 A Baquedano BAQ2838 2 8.36 369 0.212 44.74 100 16.647 11.34 19.08 24.995 10.709 no 0 +BAQ3473.1 AAGTGAAGCGAG 3473 16.374 1.29 C Baquedano BAQ3473 2 7.93 3675 0.42 82.05 100 42.09 35.37 13.46 20.69 5.12 yes 1.2 +BAQ3473.2 TGCCGCCGTAAT 3473 5.17 11.05 B Baquedano BAQ3473 2 7.93 838 0.42 82.05 100 42.09 35.37 13.46 20.69 5.12 yes 1.2 +BAQ3473.3 AACCTCGGATAA 3473 0.91 4.41 C Baquedano BAQ3473 2 7.93 16449 0.42 82.05 100 42.09 35.37 13.46 20.69 5.12 yes 1.2 +BAQ4166.1.1 GTGCTTGTGTAG 4166 33.492 3.16 C Baquedano BAQ4166 1 5.64 100 100 100 100 9.41 17.54 1.42 yes 7.1 +BAQ4166.1.2 CAACTAGACTCG 4166 16.086 18.25 B Baquedano BAQ4166 2 7.22 2085 0.084 100 100 100 100 9.41 17.54 1.42 yes 7.1 +BAQ4166.2 GGAACGACGTGA 4166 2.958 0.12 C Baquedano BAQ4166 2 7.22 3692 0.084 100 100 100 100 9.41 17.54 1.42 yes 7.1 +BAQ4166.3 TGTCAGCTGTCG 4166 28.92 0.26 C Baquedano BAQ4166 2 7.22 2271 0.084 100 100 100 100 9.41 17.54 1.42 yes 7.1 +BAQ4166.1.3 AGTGCCCTTGGT 4166 14.532 0.55 C Baquedano BAQ4166 3 7.41 100 100 100 100 9.41 17.54 1.42 yes 7.1 +BAQ4697.1 CTGGTGCTGAAT 4697 10.044 1.88 C Baquedano BAQ4697 2 7.44 424 0.055 yes 0.1 +BAQ4697.2 GACAGAGGTGCA 4697 5.864 1.22 B Baquedano BAQ4697 2 7.44 531 0.055 yes 0.1 +BAQ4697.3 TCAGACCAACTG 4697 8.264 1.39 C Baquedano BAQ4697 2 7.44 631 0.055 yes 0.1 +BAQ895.2 TCCTCACTATCA 895 0.017 1.01 B Baquedano BAQ895 2 61 2.945 32.22 43.14 25.6 0 19.17 31.82 10.54 no 0 +BAQ895.3 GCCTGCAGTACT 895 0.011 2.36 E Baquedano BAQ895 2 474 2.945 32.22 43.14 25.6 0 19.17 31.82 10.54 no 0 +YUN1005.1.1 ACGTAACCACGT 1005 0.103 13.17 I Yungay YUN1005 1 7.54 20.7 31.011 16.343 0 22.59 26.26 16.51 no 0 +YUN1005.2 TCTAACGAGTGC 1005 0.03 0.94 I Yungay YUN1005 2 160 2.27 20.7 31.011 16.343 0 22.59 26.26 16.51 no 0 +YUN1005.3 CATCTGGGCAAT 1005 0.028 4.32 I Yungay YUN1005 2 7.6 223 2.27 20.7 31.011 16.343 0 22.59 26.26 16.51 no 0 +YUN1005.1.3 GTCGGAAATTGT 1005 0.034 1.12 I Yungay YUN1005 3 7.6 20.7 31.011 16.343 0 22.59 26.26 16.51 no 0 +YUN1242.1 TGTCCGTGGATC 1242 0.228 19.2 K Yungay YUN1242 2 9 226 1.845 20.9 36.46 16.96 0 23.61 27.62 18.33 no 0 +YUN1242.2 ACTCGGCCAACT 1242 0.023 0.54 B Yungay YUN1242 2 9 194 1.845 20.9 36.46 16.96 0 23.61 27.62 18.33 no 0 +YUN1242.3 GTTGGTTGGCAT 1242 0.05 15.61 K Yungay YUN1242 2 9 452 1.845 20.9 36.46 16.96 0 23.61 27.62 18.33 no 0 +YUN1609.1 TTCCACACGTGG 1609 0.031 6.42 B Yungay YUN1609 2 8 361 0.427 17.18 50.4 12.53 0 21.47 25.39 16.1 no 0 +YUN1609.3 AACCCAGATGAT 1609 0.025 12.84 E Yungay YUN1609 2 8 424 0.427 17.18 50.4 12.53 0 21.47 25.39 16.1 no 0 +YUN2029.1 GTAGTGTCAACA 2029 0.022 9.59 K Yungay YUN2029 2 7.89 184 0.067 28.79 52.55 21.76 0 17.85 24.16 10.21 no 0 +YUN2029.2 TGGAGAGGAGAT 2029 0.232 16.71 B Yungay YUN2029 2 7.89 241 0.067 28.79 52.55 21.76 0 17.85 24.16 10.21 no 0 +YUN2029.3 CGTATAAATGCG 2029 0.078 16.14 K Yungay YUN2029 2 7.89 817 0.067 28.79 52.55 21.76 0 17.85 24.16 10.21 no 0 +YUN3008.1.1 ATCGATCCACAG 3008 0.021 1.29 G Yungay YUN3008 1 7.7 70.89 100 20.37 29.1 11.57 30.98 -2.57 no 0 +YUN3008.1.2 ACACCGCACAAT 3008 0.029 1.23 B Yungay YUN3008 2 7.71 250 2.205 70.89 100 20.37 29.1 11.57 30.98 -2.57 no 0 +YUN3008.2 GTAGCACTCATG 3008 0.036 1.1 K Yungay YUN3008 2 367 2.205 70.89 100 20.37 29.1 11.57 30.98 -2.57 no 0 +YUN3008.3 CACCTGTAGTAG 3008 0.021 1 G Yungay YUN3008 2 417 2.205 70.89 100 20.37 29.1 11.57 30.98 -2.57 no 0 +YUN3008.1.3 GTCTCCTCCCTT 3008 0.017 0.99 G Yungay YUN3008 3 7.5 70.89 100 20.37 29.1 11.57 30.98 -2.57 no 0 +YUN3153.1 AATACAGACCTG 3153 0.011 1.05 E Yungay YUN3153 2 7.6 580 2.26 59.69 93.15 32.12 0 12.5 19.62 3.48 no 0 +YUN3153.2 GACTCAACCAGT 3153 0.493 16.89 G Yungay YUN3153 2 7.6 185 2.26 59.69 93.15 32.12 0 12.5 19.62 3.48 no 0 +YUN3153.3 GGAAGAAGTAGC 3153 0.22 18.41 B Yungay YUN3153 2 7.6 391 2.26 59.69 93.15 32.12 0 12.5 19.62 3.48 no 0 +YUN3184.1 CACGAGCTACTC 3184 0.022 1.18 B Yungay YUN3184 2 7.7 254 2.235 26.97 46.57 15.09 0 14.12 25.21 2.45 no 0 +YUN3184.2 TCTCGATAAGCG 3184 0.01 1.29 E Yungay YUN3184 2 411 2.235 26.97 46.57 15.09 0 14.12 25.21 2.45 no 0 +YUN3259.1.1 TAGACACCGTGT 3259 3.71 7.07 D Yungay YUN3259 1 8.48 93.57 100 69.04 64.69 15.28 23.65 6.31 yes 2.4 +YUN3259.1.2 AGACAAGCTTCC 3259 1.543 16.92 B Yungay YUN3259 2 8.1 419 0.133 93.57 100 69.04 64.69 15.28 23.65 6.31 yes 2.4 +YUN3259.2 TCACTTGGTGCG 3259 1.935 12.11 D Yungay YUN3259 2 8.1 342 0.133 93.57 100 69.04 64.69 15.28 23.65 6.31 yes 2.4 +YUN3259.3 TTATGTACGGCG 3259 3.53 16.74 D Yungay YUN3259 2 8.1 539 0.133 93.57 100 69.04 64.69 15.28 23.65 6.31 yes 2.4 +YUN3259.1.3 TCCGCAACCTGA 3259 0.329 19.17 D Yungay YUN3259 3 8.4 93.57 100 69.04 64.69 15.28 23.65 6.31 yes 2.4 +YUN3346.1 GAGATACAGTTC 3346 0.314 16.88 D Yungay YUN3346 2 7.1 429 0.044 87.32 100 57.8 33.13 15.89 23.96 6.89 yes 0.01 +YUN3346.2 GCATGCATCCCA 3346 0.318 16.26 D Yungay YUN3346 2 7.1 666 0.044 87.32 100 57.8 33.13 15.89 23.96 6.89 yes 0.01 +YUN3346.3 GATCTAATCGAG 3346 1.218 17.14 D Yungay YUN3346 2 7.1 387 0.044 87.32 100 57.8 33.13 15.89 23.96 6.89 yes 0.01 +YUN3428.1 TACGCCCATCAG 3428 1.764 15.32 D Yungay YUN3428 2 7.2 623 0.023 99.99 100 99.91 99.42 13.61 21.09 4.13 yes 8.8 +YUN3428.2 AAGATCGTACTG 3428 1.988 6.61 D Yungay YUN3428 2 7.2 621 0.023 99.99 100 99.91 99.42 13.61 21.09 4.13 yes 8.8 +YUN3428.3 ACTCATCTTCCA 3428 2.782 15.46 D Yungay YUN3428 2 7.2 658 0.023 99.99 100 99.91 99.42 13.61 21.09 4.13 yes 8.8 +YUN3533.1.1 TTGGACGTCCAC 3533 3.352 14.29 D Yungay YUN3533 1 7.1 100 100 99.93 99.94 11.41 19.21 3.47 yes 8.6 +YUN3533.1.2 TCCAGGGCTATA 3533 3.21 14.32 D Yungay YUN3533 2 8 521 0.024 100 100 99.93 99.94 11.41 19.21 3.47 yes 8.6 +YUN3533.2 GAAACTCCTAGA 3533 9.236 14.33 D Yungay YUN3533 2 8 773 0.024 100 100 99.93 99.94 11.41 19.21 3.47 yes 8.6 +YUN3533.3 ATCGGGCTTAAC 3533 3.642 17.43 D Yungay YUN3533 2 8 664 0.024 100 100 99.93 99.94 11.41 19.21 3.47 yes 8.6 +YUN3533.1.3 GCGTAGAGAGAC 3533 1.987 7.55 D Yungay YUN3533 3 7.8 100 100 99.93 99.94 11.41 19.21 3.47 yes 8.6 +YUN3856.1.1 AATCTTGCGCCG 3856 6.444 12.93 G Yungay YUN3856 1 6.98 99.44 100 73.75 93.7 9.51 17.45 0.45 yes 3.1 +YUN3856.1.2 GGAAATCCCATC 3856 6.23 16.35 G Yungay YUN3856 2 7.43 713 0.029 99.44 100 73.75 93.7 9.51 17.45 0.45 yes 3.1 +YUN3856.2 TTGGAACGGCTT 3856 4.178 17.12 H Yungay YUN3856 2 7.43 404 0.029 99.44 100 73.75 93.7 9.51 17.45 0.45 yes 3.1 +YUN3856.3 TCCTAGGTCCGA 3856 6.695 15.86 H Yungay YUN3856 2 7.43 988 0.029 99.44 100 73.75 93.7 9.51 17.45 0.45 yes 3.1 +YUN3856.1.3 GACCGTCAATAC 3856 3.134 18.17 G Yungay YUN3856 3 7.54 99.44 100 73.75 93.7 9.51 17.45 0.45 yes 3.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demux_single.test0.md.tsv Fri Jan 13 22:41:40 2023 +0000 @@ -0,0 +1,11 @@ +#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description +#q2:types categorical categorical categorical numeric categorical +PC.354 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse_I.D._354 +PC.355 AACTCGTCGATG YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse_I.D._355 +PC.356 ACAGACCACTCA YATGCTGCCTCCCGTAGGAGT Control 20061126 Control_mouse_I.D._356 +PC.481 ACCAGCGACTAG YATGCTGCCTCCCGTAGGAGT Control 20070314 Control_mouse_I.D._481 +PC.593 AGCAGCACTTGT YATGCTGCCTCCCGTAGGAGT Control 20071210 Control_mouse_I.D._593 +PC.607 AACTGTGCGTAC YATGCTGCCTCCCGTAGGAGT Fast 20071112 Fasting_mouse_I.D._607 +PC.634 ACAGAGTCGGCT YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._634 +PC.635 ACCGCAGAGTCA YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._635 +PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._636