| Previous changeset 0:f003ba94e4fe (2022-08-29) Next changeset 2:c6a8822e19f2 (2023-06-08) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732 |
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modified:
qiime2__cutadapt__demux_paired.xml |
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added:
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 |
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removed:
test-data/.gitkeep |
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| diff -r f003ba94e4fe -r d58b93d0a723 qiime2__cutadapt__demux_paired.xml --- a/qiime2__cutadapt__demux_paired.xml Mon Aug 29 19:22:08 2022 +0000 +++ b/qiime2__cutadapt__demux_paired.xml Fri Jan 13 22:41:52 2023 +0000 |
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| @@ -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 demux-paired" id="qiime2__cutadapt__demux_paired" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> <description>Demultiplex paired-end sequence data with barcodes in-sequence.</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 demux_paired '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run cutadapt demux_paired '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -77,7 +77,30 @@ <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/> <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/> </outputs> - <tests/> + <tests> + <test> + <param name="seqs" value="demux_paired.test0.seqs.qza" ftype="qza"/> + <conditional name="forward_barcodes"> + <param name="type" value="tsv"/> + <param name="source" value="demux_paired.test0.md.tsv" ftype="qiime2.tabular"/> + <param name="column" value="2"/> + </conditional> + <output name="per_sample_sequences" ftype="qza"> + <assert_contents> + <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> + <has_line_matching expression="type: SampleData\[PairedEndSequencesWithQuality\]"/> + </has_archive_member> + </assert_contents> + </output> + <output name="untrimmed_sequences" ftype="qza"> + <assert_contents> + <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> + <has_line_matching expression="type: MultiplexedPairedEndBarcodeInSequence"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: cutadapt demux-paired ============================== @@ -95,6 +118,22 @@ ------------ Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes are expected to be located within the sequence data (versus the header, or a separate barcode file). +Examples: +--------- + +paired +****** +Using the ``qiime2 cutadapt demux-paired`` tool: + #. Set *"seqs"* to ``#: seqs.qza`` + #. For *"forward_barcodes"*: + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``md.tsv`` + #. Set *"Column Name"* to ``barcode-sequence`` + + #. Press the ``Execute`` button. + + | |
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| diff -r f003ba94e4fe -r d58b93d0a723 test-data/demux_paired.test0.md.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demux_paired.test0.md.tsv Fri Jan 13 22:41:52 2023 +0000 |
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| b'@@ -0,0 +1,77 @@\n+sample-id\tbarcode-sequence\televation\textract-concen\tamplicon-concentration\textract-group-no\ttransect-name\tsite-name\tdepth\tph\ttoc\tec\taverage-soil-relative-humidity\trelative-humidity-soil-high\trelative-humidity-soil-low\tpercent-relative-humidity-soil-100\taverage-soil-temperature\ttemperature-soil-high\ttemperature-soil-low\tvegetation\tpercentcover\r\n+#q2:types\tcategorical\tnumeric\tnumeric\tnumeric\tcategorical\tcategorical\tcategorical\tnumeric\tnumeric\tnumeric\tnumeric\tnumeric\tnumeric\tnumeric\tnumeric\tnumeric\tnumeric\tnumeric\tcategorical\tnumeric\r\n+BAQ1370.1.2\tGCCCAAGTTCAC\t1370\t0.019\t0.95\tB\tBaquedano\tBAQ1370\t2\t7.98\t525\t6.08\t16.17\t23.97\t11.42\t0\t22.61\t35.21\t12.46\tno\t0\r\n+BAQ1370.3\tGCGCCGAATCTT\t1370\t0.124\t17.46\tE\tBaquedano\tBAQ1370\t2\t\t771\t6.08\t16.17\t23.97\t11.42\t0\t22.61\t35.21\t12.46\tno\t0\r\n+BAQ1370.1.3\tATAAAGAGGAGG\t1370\t1.2\t0.96\tJ\tBaquedano\tBAQ1370\t3\t8.13\t\t\t16.17\t23.97\t11.42\t0\t22.61\t35.21\t12.46\tno\t0\r\n+BAQ1552.1.1\tATCCCAGCATGC\t1552\t0.722\t18.83\tJ\tBaquedano\tBAQ1552\t1\t7.87\t\t\t15.75\t35.36\t11.1\t0\t22.63\t30.65\t10.96\tno\t0\r\n+BAQ1552.2\tGCTTCCAGACAA\t1552\t0.017\t2\tB\tBaquedano\tBAQ1552\t2\t\t223\t1.839\t15.75\t35.36\t11.1\t0\t22.63\t30.65\t10.96\tno\t0\r\n+BAQ2420.1.1\tACACAGTCCTGA\t2420\t0.35\t7.4\tH\tBaquedano\tBAQ2420\t1\t9.33\t\t\t82.54\t100\t41.135\t46.77\t22.45\t28.297\t13.294\tno\t0\r\n+BAQ2420.1.2\tATTATACGGCGC\t2420\t0.108\t11.42\tH\tBaquedano\tBAQ2420\t2\t9.36\t166\t0.075\t82.54\t100\t41.135\t46.77\t22.45\t28.297\t13.294\tno\t0\r\n+BAQ2420.2\tTAAACGCGACTC\t2420\t0.089\t10.06\tA\tBaquedano\tBAQ2420\t2\t9.36\t337\t0.075\t82.54\t100\t41.135\t46.77\t22.45\t28.297\t13.294\tno\t0\r\n+BAQ2420.3\tCCTCGGGTACTA\t2420\t0.083\t15.92\tC\tBaquedano\tBAQ2420\t2\t9.36\t574\t0.075\t82.54\t100\t41.135\t46.77\t22.45\t28.297\t13.294\tno\t0\r\n+BAQ2420.1.3\tATTCAGATGGCA\t2420\t0.132\t10\tH\tBaquedano\tBAQ2420\t3\t8.9\t\t\t82.54\t100\t41.135\t46.77\t22.45\t28.297\t13.294\tno\t0\r\n+BAQ2462.1\tTTCACCTGTATC\t2462\t1.166\t15.29\tH\tBaquedano\tBAQ2462\t2\t8.35\t173\t0.506\t69.08\t98.396\t32.558\t0.21\t21.83\t29.024\t12.971\tno\t0\r\n+BAQ2462.2\tCTCCAGGTCATG\t2462\t0.049\t10.39\tH\tBaquedano\tBAQ2462\t2\t8.35\t331\t0.506\t69.08\t98.396\t32.558\t0.21\t21.83\t29.024\t12.971\tno\t0\r\n+BAQ2462.3\tCAGGATTCGTAC\t2462\t0.066\t8.46\tA\tBaquedano\tBAQ2462\t2\t8.35\t634\t0.506\t69.08\t98.396\t32.558\t0.21\t21.83\t29.024\t12.971\tno\t0\r\n+BAQ2687.1\tGTGGCCTACTAC\t2687\t1.223\t1.24\tA\tBaquedano\tBAQ2687\t2\t8.35\t554\t0.131\t73.21\t100\t20.87\t43.48\t18.2\t25\t10.67\tyes\t0.1\r\n+BAQ2687.2\tTTCCCTTCTCCG\t2687\t0.251\t17.53\tC\tBaquedano\tBAQ2687\t2\t8.35\t350\t0.131\t73.21\t100\t20.87\t43.48\t18.2\t25\t10.67\tyes\t0.1\r\n+BAQ2687.3\tCATTTGACGACG\t2687\t1.176\t12.1\tE\tBaquedano\tBAQ2687\t2\t8.35\t400\t0.131\t73.21\t100\t20.87\t43.48\t18.2\t25\t10.67\tyes\t0.1\r\n+BAQ2838.1\tCGCATACGACCT\t2838\t0.467\t10.91\tG\tBaquedano\tBAQ2838\t2\t8.36\t353\t0.212\t44.74\t100\t16.647\t11.34\t19.08\t24.995\t10.709\tno\t0\r\n+BAQ2838.2\tGCCTCGTACTGA\t2838\t0.309\t14.38\tH\tBaquedano\tBAQ2838\t2\t8.36\t260\t0.212\t44.74\t100\t16.647\t11.34\t19.08\t24.995\t10.709\tno\t0\r\n+BAQ2838.3\tACCAACAGATTG\t2838\t0.145\t14.06\tA\tBaquedano\tBAQ2838\t2\t8.36\t369\t0.212\t44.74\t100\t16.647\t11.34\t19.08\t24.995\t10.709\tno\t0\r\n+BAQ3473.1\tAAGTGAAGCGAG\t3473\t16.374\t1.29\tC\tBaquedano\tBAQ3473\t2\t7.93\t3675\t0.42\t82.05\t100\t42.09\t35.37\t13.46\t20.69\t5.12\tyes\t1.2\r\n+BAQ3473.2\tTGCCGCCGTAAT\t3473\t5.17\t11.05\tB\tBaquedano\tBAQ3473\t2\t7.93\t838\t0.42\t82.05\t100\t42.09\t35.37\t13.46\t20.69\t5.12\tyes\t1.2\r\n+BAQ3473.3\tAACCTCGGATAA\t3473\t0.91\t4.41\tC\tBaquedano\tBAQ3473\t2\t7.93\t16449\t0.42\t82.05\t100\t42.09\t35.37\t13.46\t20.69\t5.12\tyes\t1.2\r\n+BAQ4166.1.1\tGTGCTTGTGTAG\t4166\t33.492\t3.16\tC\tBaquedano\tBAQ4166\t1\t5.64\t\t\t100\t100\t100\t100\t9.41\t17.54\t1.42\tyes\t7.1\r\n+BAQ4166.1.2\tCAACTAGACTCG\t4166\t16.086\t18.25\tB\tBaquedano\tBAQ4166\t2\t7.22\t2085\t0.084\t100\t100\t100\t100\t9.41\t17.54\t1.42\tyes\t7.1\r\n+BAQ4166.2\tGGAACGACGTGA\t4166\t2.958\t0.12\tC\tBaquedano\tBAQ4166\t2\t7.22\t3692\t0.084\t100\t100\t100\t100\t9.41\t17.54\t1.42\tyes\t7.1\r\n+BAQ4166.3\tTGTCAGCTGTCG\t4166\t28.92\t0.26\tC\tBaquedano\tBAQ4166\t2\t7.22\t2271\t0.084\t100\t100\t100\t100\t9.41\t17.54\t1.42\tyes\t7.1\r\n+BAQ4166.1.3\tAGTGCCCTTGGT\t4166\t14.532\t0.55\tC\tBaquedano\tBAQ4166\t3\t7.41\t\t\t100\t100\t100\t100\t9.41\t17.54\t1.42\tyes\t7.1\r\n+BAQ4697.1\tCTGGTGCTGAAT\t4697\t10.044\t1.88\tC\tBaquedano\tBAQ4697\t2\t7.44\t424\t0.055\t\t\t\t\t\t\t\tyes\t0.1\r\n+BAQ4697.2\tGACAGAGGTGCA\t4697\t5.864\t1.22\tB\tBaquedano\tBAQ'..b'2029.1\tGTAGTGTCAACA\t2029\t0.022\t9.59\tK\tYungay\tYUN2029\t2\t7.89\t184\t0.067\t28.79\t52.55\t21.76\t0\t17.85\t24.16\t10.21\tno\t0\r\n+YUN2029.2\tTGGAGAGGAGAT\t2029\t0.232\t16.71\tB\tYungay\tYUN2029\t2\t7.89\t241\t0.067\t28.79\t52.55\t21.76\t0\t17.85\t24.16\t10.21\tno\t0\r\n+YUN2029.3\tCGTATAAATGCG\t2029\t0.078\t16.14\tK\tYungay\tYUN2029\t2\t7.89\t817\t0.067\t28.79\t52.55\t21.76\t0\t17.85\t24.16\t10.21\tno\t0\r\n+YUN3008.1.1\tATCGATCCACAG\t3008\t0.021\t1.29\tG\tYungay\tYUN3008\t1\t7.7\t\t\t70.89\t100\t20.37\t29.1\t11.57\t30.98\t-2.57\tno\t0\r\n+YUN3008.1.2\tACACCGCACAAT\t3008\t0.029\t1.23\tB\tYungay\tYUN3008\t2\t7.71\t250\t2.205\t70.89\t100\t20.37\t29.1\t11.57\t30.98\t-2.57\tno\t0\r\n+YUN3008.2\tGTAGCACTCATG\t3008\t0.036\t1.1\tK\tYungay\tYUN3008\t2\t\t367\t2.205\t70.89\t100\t20.37\t29.1\t11.57\t30.98\t-2.57\tno\t0\r\n+YUN3008.3\tCACCTGTAGTAG\t3008\t0.021\t1\tG\tYungay\tYUN3008\t2\t\t417\t2.205\t70.89\t100\t20.37\t29.1\t11.57\t30.98\t-2.57\tno\t0\r\n+YUN3008.1.3\tGTCTCCTCCCTT\t3008\t0.017\t0.99\tG\tYungay\tYUN3008\t3\t7.5\t\t\t70.89\t100\t20.37\t29.1\t11.57\t30.98\t-2.57\tno\t0\r\n+YUN3153.1\tAATACAGACCTG\t3153\t0.011\t1.05\tE\tYungay\tYUN3153\t2\t7.6\t580\t2.26\t59.69\t93.15\t32.12\t0\t12.5\t19.62\t3.48\tno\t0\r\n+YUN3153.2\tGACTCAACCAGT\t3153\t0.493\t16.89\tG\tYungay\tYUN3153\t2\t7.6\t185\t2.26\t59.69\t93.15\t32.12\t0\t12.5\t19.62\t3.48\tno\t0\r\n+YUN3153.3\tGGAAGAAGTAGC\t3153\t0.22\t18.41\tB\tYungay\tYUN3153\t2\t7.6\t391\t2.26\t59.69\t93.15\t32.12\t0\t12.5\t19.62\t3.48\tno\t0\r\n+YUN3184.1\tCACGAGCTACTC\t3184\t0.022\t1.18\tB\tYungay\tYUN3184\t2\t7.7\t254\t2.235\t26.97\t46.57\t15.09\t0\t14.12\t25.21\t2.45\tno\t0\r\n+YUN3184.2\tTCTCGATAAGCG\t3184\t0.01\t1.29\tE\tYungay\tYUN3184\t2\t\t411\t2.235\t26.97\t46.57\t15.09\t0\t14.12\t25.21\t2.45\tno\t0\r\n+YUN3259.1.1\tTAGACACCGTGT\t3259\t3.71\t7.07\tD\tYungay\tYUN3259\t1\t8.48\t\t\t93.57\t100\t69.04\t64.69\t15.28\t23.65\t6.31\tyes\t2.4\r\n+YUN3259.1.2\tAGACAAGCTTCC\t3259\t1.543\t16.92\tB\tYungay\tYUN3259\t2\t8.1\t419\t0.133\t93.57\t100\t69.04\t64.69\t15.28\t23.65\t6.31\tyes\t2.4\r\n+YUN3259.2\tTCACTTGGTGCG\t3259\t1.935\t12.11\tD\tYungay\tYUN3259\t2\t8.1\t342\t0.133\t93.57\t100\t69.04\t64.69\t15.28\t23.65\t6.31\tyes\t2.4\r\n+YUN3259.3\tTTATGTACGGCG\t3259\t3.53\t16.74\tD\tYungay\tYUN3259\t2\t8.1\t539\t0.133\t93.57\t100\t69.04\t64.69\t15.28\t23.65\t6.31\tyes\t2.4\r\n+YUN3259.1.3\tTCCGCAACCTGA\t3259\t0.329\t19.17\tD\tYungay\tYUN3259\t3\t8.4\t\t\t93.57\t100\t69.04\t64.69\t15.28\t23.65\t6.31\tyes\t2.4\r\n+YUN3346.1\tGAGATACAGTTC\t3346\t0.314\t16.88\tD\tYungay\tYUN3346\t2\t7.1\t429\t0.044\t87.32\t100\t57.8\t33.13\t15.89\t23.96\t6.89\tyes\t0.01\r\n+YUN3346.2\tGCATGCATCCCA\t3346\t0.318\t16.26\tD\tYungay\tYUN3346\t2\t7.1\t666\t0.044\t87.32\t100\t57.8\t33.13\t15.89\t23.96\t6.89\tyes\t0.01\r\n+YUN3346.3\tGATCTAATCGAG\t3346\t1.218\t17.14\tD\tYungay\tYUN3346\t2\t7.1\t387\t0.044\t87.32\t100\t57.8\t33.13\t15.89\t23.96\t6.89\tyes\t0.01\r\n+YUN3428.1\tTACGCCCATCAG\t3428\t1.764\t15.32\tD\tYungay\tYUN3428\t2\t7.2\t623\t0.023\t99.99\t100\t99.91\t99.42\t13.61\t21.09\t4.13\tyes\t8.8\r\n+YUN3428.2\tAAGATCGTACTG\t3428\t1.988\t6.61\tD\tYungay\tYUN3428\t2\t7.2\t621\t0.023\t99.99\t100\t99.91\t99.42\t13.61\t21.09\t4.13\tyes\t8.8\r\n+YUN3428.3\tACTCATCTTCCA\t3428\t2.782\t15.46\tD\tYungay\tYUN3428\t2\t7.2\t658\t0.023\t99.99\t100\t99.91\t99.42\t13.61\t21.09\t4.13\tyes\t8.8\r\n+YUN3533.1.1\tTTGGACGTCCAC\t3533\t3.352\t14.29\tD\tYungay\tYUN3533\t1\t7.1\t\t\t100\t100\t99.93\t99.94\t11.41\t19.21\t3.47\tyes\t8.6\r\n+YUN3533.1.2\tTCCAGGGCTATA\t3533\t3.21\t14.32\tD\tYungay\tYUN3533\t2\t8\t521\t0.024\t100\t100\t99.93\t99.94\t11.41\t19.21\t3.47\tyes\t8.6\r\n+YUN3533.2\tGAAACTCCTAGA\t3533\t9.236\t14.33\tD\tYungay\tYUN3533\t2\t8\t773\t0.024\t100\t100\t99.93\t99.94\t11.41\t19.21\t3.47\tyes\t8.6\r\n+YUN3533.3\tATCGGGCTTAAC\t3533\t3.642\t17.43\tD\tYungay\tYUN3533\t2\t8\t664\t0.024\t100\t100\t99.93\t99.94\t11.41\t19.21\t3.47\tyes\t8.6\r\n+YUN3533.1.3\tGCGTAGAGAGAC\t3533\t1.987\t7.55\tD\tYungay\tYUN3533\t3\t7.8\t\t\t100\t100\t99.93\t99.94\t11.41\t19.21\t3.47\tyes\t8.6\r\n+YUN3856.1.1\tAATCTTGCGCCG\t3856\t6.444\t12.93\tG\tYungay\tYUN3856\t1\t6.98\t\t\t99.44\t100\t73.75\t93.7\t9.51\t17.45\t0.45\tyes\t3.1\r\n+YUN3856.1.2\tGGAAATCCCATC\t3856\t6.23\t16.35\tG\tYungay\tYUN3856\t2\t7.43\t713\t0.029\t99.44\t100\t73.75\t93.7\t9.51\t17.45\t0.45\tyes\t3.1\r\n+YUN3856.2\tTTGGAACGGCTT\t3856\t4.178\t17.12\tH\tYungay\tYUN3856\t2\t7.43\t404\t0.029\t99.44\t100\t73.75\t93.7\t9.51\t17.45\t0.45\tyes\t3.1\r\n+YUN3856.3\tTCCTAGGTCCGA\t3856\t6.695\t15.86\tH\tYungay\tYUN3856\t2\t7.43\t988\t0.029\t99.44\t100\t73.75\t93.7\t9.51\t17.45\t0.45\tyes\t3.1\r\n+YUN3856.1.3\tGACCGTCAATAC\t3856\t3.134\t18.17\tG\tYungay\tYUN3856\t3\t7.54\t\t\t99.44\t100\t73.75\t93.7\t9.51\t17.45\t0.45\tyes\t3.1\r\n' 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| diff -r f003ba94e4fe -r d58b93d0a723 test-data/demux_single.test0.md.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demux_single.test0.md.tsv Fri Jan 13 22:41:52 2023 +0000 |
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| @@ -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 |
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