diff qiime2__cutadapt__demux_paired.xml @ 0:f003ba94e4fe draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

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+++ b/qiime2__cutadapt__demux_paired.xml	Mon Aug 29 19:22:08 2022 +0000
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+<?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 &quot;too many files&quot; errors related to sample quantity. Set to &quot;0&quot; 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>