| Next changeset 1:d58b93d0a723 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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qiime2__cutadapt__demux_paired.xml test-data/.gitkeep |
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| diff -r 000000000000 -r f003ba94e4fe qiime2__cutadapt__demux_paired.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__cutadapt__demux_paired.xml Mon Aug 29 19:22:08 2022 +0000 |
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| @@ -0,0 +1,106 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2022, 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) +for: + qiime2 (version: 2022.8.1) +--> +<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"> + <description>Demultiplex paired-end sequence data with barcodes in-sequence.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version cutadapt</version_command> + <command detect_errors="aggressive">q2galaxy run cutadapt demux_paired '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="seqs" type="data" format="qza" label="seqs: MultiplexedPairedEndBarcodeInSequence" help="[required] The paired-end sequences to be demultiplexed."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="MultiplexedPairedEndBarcodeInSequence"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['MultiplexedPairedEndBarcodeInSequence']</validator> + </param> + <conditional name="forward_barcodes"> + <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."> + <option value="tsv" selected="true">Metadata from TSV</option> + <option value="qza">Metadata from Artifact</option> + </param> + <when value="tsv"> + <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> + <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> + <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> + </param> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + <param name="column" type="text" label="Column Name"> + <validator type="empty_field"/> + </param> + </when> + </conditional> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <conditional name="reverse_barcodes"> + <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."> + <option value="none" selected="true">None (default)</option> + <option value="tsv">Metadata from TSV</option> + <option value="qza">Metadata from Artifact</option> + </param> + <when value="none"/> + <when value="tsv"> + <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> + <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> + <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> + </param> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + <param name="column" type="text" label="Column Name"> + <validator type="empty_field"/> + </param> + </when> + </conditional> + <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."/> + <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."/> + <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="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)."/> + <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1] Number of CPU cores to use."/> + </section> + </inputs> + <outputs> + <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/> + <help> +QIIME 2: cutadapt demux-paired +============================== +Demultiplex paired-end sequence data with barcodes in-sequence. + + +Outputs: +-------- +:per_sample_sequences.qza: The resulting demultiplexed sequences. +:untrimmed_sequences.qza: The sequences that were unmatched to barcodes. + +| + +Description: +------------ +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). + + +| + +</help> + <citations> + <citation type="doi">10.14806/ej.17.1.200</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool> |