Mercurial > repos > q2d2 > qiime2__cutadapt__demux_paired
annotate qiime2__cutadapt__demux_paired.xml @ 1:d58b93d0a723 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 22:41:52 +0000 |
| parents | f003ba94e4fe |
| children | c6a8822e19f2 |
| rev | line source |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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1
d58b93d0a723
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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3 Copyright (c) 2023, QIIME 2 development team. |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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d58b93d0a723
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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9 q2galaxy (version: 2022.11.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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d58b93d0a723
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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11 qiime2 (version: 2022.11.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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1
d58b93d0a723
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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13 <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"> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Demultiplex paired-end sequence data with barcodes in-sequence.</description> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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1
d58b93d0a723
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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16 <container type="docker">quay.io/qiime2/core:2022.11</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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17 </requirements> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <version_command>q2galaxy version cutadapt</version_command> |
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1
d58b93d0a723
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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19 <command detect_errors="exit_code">q2galaxy run cutadapt demux_paired '$inputs'</command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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20 <configfiles> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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21 <inputs name="inputs" data_style="paths"/> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <inputs> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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24 <param name="seqs" type="data" format="qza" label="seqs: MultiplexedPairedEndBarcodeInSequence" help="[required] The paired-end sequences to be demultiplexed."> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 <options options_filter_attribute="metadata.semantic_type"> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="MultiplexedPairedEndBarcodeInSequence"/> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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27 </options> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['MultiplexedPairedEndBarcodeInSequence']</validator> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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29 </param> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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30 <conditional name="forward_barcodes"> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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31 <param name="type" type="select" label="forward_barcodes: MetadataColumn[Categorical]" help="[required] The sample metadata column listing the per-sample barcodes for the forward reads."> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 <option value="tsv" selected="true">Metadata from TSV</option> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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33 <option value="qza">Metadata from Artifact</option> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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34 </param> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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35 <when value="tsv"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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36 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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37 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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38 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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39 </param> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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40 </when> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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41 <when value="qza"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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42 <param name="source" type="data" format="qza" label="Metadata Source"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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43 <param name="column" type="text" label="Column Name"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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44 <validator type="empty_field"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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45 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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46 </when> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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47 </conditional> |
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48 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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49 <conditional name="reverse_barcodes"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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50 <param name="type" type="select" label="reverse_barcodes: MetadataColumn[Categorical]" help="[optional] The sample metadata column listing the per-sample barcodes for the reverse reads."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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51 <option value="none" selected="true">None (default)</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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52 <option value="tsv">Metadata from TSV</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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53 <option value="qza">Metadata from Artifact</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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54 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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55 <when value="none"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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56 <when value="tsv"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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57 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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58 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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59 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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60 </param> |
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61 </when> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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62 <when value="qza"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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63 <param name="source" type="data" format="qza" label="Metadata Source"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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64 <param name="column" type="text" label="Column Name"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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65 <validator type="empty_field"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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66 </param> |
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67 </when> |
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68 </conditional> |
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69 <param name="error_rate" type="float" min="0" max="1" value="0.1" label="error_rate: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.1] The level of error tolerance, specified as the maximum allowable error rate."/> |
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70 <param name="batch_size" type="integer" min="0" value="0" label="batch_size: Int % Range(0, None)" help="[default: 0] The number of samples cutadapt demultiplexes concurrently. Demultiplexing in smaller batches will yield the same result with marginal speed loss, and may solve "too many files" errors related to sample quantity. Set to "0" to process all samples at once."/> |
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71 <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."/> |
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72 <param name="mixed_orientation" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="mixed_orientation: Bool" help="[default: No] Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file)."/> |
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73 <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1] Number of CPU cores to use."/> |
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74 </section> |
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75 </inputs> |
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76 <outputs> |
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77 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/> |
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78 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/> |
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79 </outputs> |
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1
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80 <tests> |
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81 <test> |
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82 <param name="seqs" value="demux_paired.test0.seqs.qza" ftype="qza"/> |
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83 <conditional name="forward_barcodes"> |
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84 <param name="type" value="tsv"/> |
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85 <param name="source" value="demux_paired.test0.md.tsv" ftype="qiime2.tabular"/> |
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86 <param name="column" value="2"/> |
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87 </conditional> |
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88 <output name="per_sample_sequences" ftype="qza"> |
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89 <assert_contents> |
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90 <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"> |
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91 <has_line_matching expression="type: SampleData\[PairedEndSequencesWithQuality\]"/> |
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92 </has_archive_member> |
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93 </assert_contents> |
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94 </output> |
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95 <output name="untrimmed_sequences" ftype="qza"> |
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96 <assert_contents> |
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97 <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"> |
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98 <has_line_matching expression="type: MultiplexedPairedEndBarcodeInSequence"/> |
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99 </has_archive_member> |
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100 </assert_contents> |
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101 </output> |
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102 </test> |
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103 </tests> |
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104 <help> |
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105 QIIME 2: cutadapt demux-paired |
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106 ============================== |
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107 Demultiplex paired-end sequence data with barcodes in-sequence. |
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108 |
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109 |
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110 Outputs: |
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111 -------- |
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112 :per_sample_sequences.qza: The resulting demultiplexed sequences. |
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113 :untrimmed_sequences.qza: The sequences that were unmatched to barcodes. |
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114 |
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115 | |
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116 |
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117 Description: |
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118 ------------ |
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119 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). |
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120 |
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121 Examples: |
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122 --------- |
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123 |
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124 paired |
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125 ****** |
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126 Using the ``qiime2 cutadapt demux-paired`` tool: |
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127 #. Set *"seqs"* to ``#: seqs.qza`` |
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128 #. For *"forward_barcodes"*: |
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129 |
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130 #. Leave as ``Metadata from TSV`` |
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131 #. Set *"Metadata Source"* to ``md.tsv`` |
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132 #. Set *"Column Name"* to ``barcode-sequence`` |
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133 |
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134 #. Press the ``Execute`` button. |
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135 |
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136 |
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137 |
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138 | |
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139 |
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140 </help> |
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141 <citations> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
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142 <citation type="doi">10.14806/ej.17.1.200</citation> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
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143 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
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144 </citations> |
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f003ba94e4fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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145 </tool> |