Mercurial > repos > q2d2 > qiime2__rescript__orient_seqs

changeset 0:4d99cfa5fac1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:23:41 +0000
parents
children daf6c330ff82
files qiime2__rescript__orient_seqs.xml test-data/.gitkeep
diffstat 1 files changed, 123 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__rescript__orient_seqs.xml	Thu Apr 25 21:23:41 2024 +0000
@@ -0,0 +1,123 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2024, 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: 2024.2.1)
+for:
+    qiime2 (version: 2024.2.0)
+-->
+<tool name="qiime2 rescript orient-seqs" id="qiime2__rescript__orient_seqs" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Orient input sequences by comparison against reference.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+    </requirements>
+    <version_command>q2galaxy version rescript</version_command>
+    <command detect_errors="exit_code">q2galaxy run rescript orient_seqs '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  Sequences to be oriented.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Sequence]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="reference_sequences" type="data" format="qza" optional="true" label="reference_sequences: FeatureData[Sequence]" help="[optional]  Reference sequences to orient against. If no reference is provided, all the sequences will be reverse complemented and all parameters will be ignored.">
+                <options options_filter_attribute="metadata.semantic_type">
+                    <filter type="add_value" value="FeatureData[Sequence]"/>
+                </options>
+                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
+            </param>
+            <param name="threads" type="integer" min="1" max="255" value="1" label="threads: Int % Range(1, 256)" help="[default: 1]  Number of computation threads to use (1 to 256). The number of threads should be lesser or equal to the number of available CPU cores."/>
+            <param name="dbmask" type="select" label="dbmask: Str % Choices('none', 'dust', 'soft')" display="radio">
+                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                <option value="none">none</option>
+                <option value="dust">dust</option>
+                <option value="soft">soft</option>
+            </param>
+            <conditional name="__q2galaxy__GUI__conditional__relabel__" label="relabel: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="relabel: Str" help="[optional]  Relabel sequences using the prefix string and a ticker (1, 2, 3, etc.) to construct the new headers. Use --sizeout to conserve the abundance annotations.">
+                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
+                    <option value="__q2galaxy__::control::provide">Provide a value</option>
+                </param>
+                <when value="__q2galaxy__::control::default">
+                    <param name="relabel" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="relabel" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <param name="relabel_keep" type="select" label="relabel_keep: Bool" help="[optional]  When relabeling, keep the original identifier in the header after a space." display="radio">
+                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                <option value="__q2galaxy__::literal::True">Yes</option>
+                <option value="__q2galaxy__::literal::False">No</option>
+            </param>
+            <param name="relabel_md5" type="select" label="relabel_md5: Bool" help="[optional]  When relabeling, use the MD5 digest of the sequence as the new identifier. Use --sizeout to conserve the abundance annotations." display="radio">
+                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                <option value="__q2galaxy__::literal::True">Yes</option>
+                <option value="__q2galaxy__::literal::False">No</option>
+            </param>
+            <param name="relabel_self" type="select" label="relabel_self: Bool" help="[optional]  Relabel sequences using the sequence itself as a label." display="radio">
+                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                <option value="__q2galaxy__::literal::True">Yes</option>
+                <option value="__q2galaxy__::literal::False">No</option>
+            </param>
+            <param name="relabel_sha1" type="select" label="relabel_sha1: Bool" help="[optional]  When relabeling, use the SHA1 digest of the sequence as the new identifier. The probability of a collision is smaller than the MD5 algorithm." display="radio">
+                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                <option value="__q2galaxy__::literal::True">Yes</option>
+                <option value="__q2galaxy__::literal::False">No</option>
+            </param>
+            <param name="sizein" type="select" label="sizein: Bool" help="[optional]  In de novo mode, abundance annotations (pattern `[&gt;;]size=integer[;]`) present in sequence headers are taken into account." display="radio">
+                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                <option value="__q2galaxy__::literal::True">Yes</option>
+                <option value="__q2galaxy__::literal::False">No</option>
+            </param>
+            <param name="sizeout" type="select" label="sizeout: Bool" help="[optional]  Add abundance annotations to the output FASTA files." display="radio">
+                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                <option value="__q2galaxy__::literal::True">Yes</option>
+                <option value="__q2galaxy__::literal::False">No</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="oriented_seqs" format="qza" label="${tool.name} on ${on_string}: oriented_seqs.qza" from_work_dir="oriented_seqs.qza"/>
+        <data name="unmatched_seqs" format="qza" label="${tool.name} on ${on_string}: unmatched_seqs.qza" from_work_dir="unmatched_seqs.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript orient-seqs
+=============================
+Orient input sequences by comparison against reference.
+
+
+Outputs:
+--------
+:oriented_seqs.qza: Query sequences in same orientation as top matching reference sequence.
+:unmatched_seqs.qza: Query sequences that fail to match at least one reference sequence in either + or - orientation. This will be empty if no refrence is provided.
+
+|  
+
+Description:
+------------
+Orient input sequences by comparison against a set of reference sequences using VSEARCH. This action can also be used to quickly filter out sequences that (do not) match a set of reference sequences in either orientation. Alternatively, if no reference sequences are provided as input, all input sequences will be reverse-complemented. In this case, no alignment is performed, and all alignment parameters (`dbmask`, `relabel`, `relabel_keep`, `relabel_md5`, `relabel_self`, `relabel_sha1`, `sizein`, `sizeout` and `threads`) are ignored.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.7717/peerj.2584</citation>
+        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>