Mercurial > repos > q2d2 > qiime2__alignment__mafft_add

comparison qiime2__alignment__mafft_add.xml @ 7:b413f3a44b8d draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9436cc47c72b58a6a3d3a5c2ee075689c2926ef0
author q2d2
date Tue, 15 Jul 2025 21:43:13 +0000
parents 4ea333b09d2c
children
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6:4ea333b09d2c 7:b413f3a44b8d
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2025.4.0) 9 q2galaxy (version: 2025.7.0)
10 for: 10 for:
11 qiime2 (version: 2025.4.0) 11 qiime2 (version: 2025.7.0)
12 --> 12 -->
13 <tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause">
14 <description>Add sequences to multiple sequence alignment with MAFFT.</description> 14 <description>Add sequences to multiple sequence alignment with MAFFT.</description>
15 <xrefs> 15 <xrefs>
16 <xref type="bio.tools">qiime2</xref> 16 <xref type="bio.tools">qiime2</xref>
17 </xrefs> 17 </xrefs>
18 <requirements> 18 <requirements>
19 <container type="docker">quay.io/qiime2/amplicon:2025.4</container> 19 <container type="docker">quay.io/qiime2/amplicon:2025.7</container>
20 </requirements> 20 </requirements>
21 <version_command>q2galaxy version alignment</version_command> 21 <version_command>q2galaxy version alignment</version_command>
22 <command detect_errors="exit_code">q2galaxy run alignment mafft_add '$inputs'</command> 22 <command detect_errors="exit_code">q2galaxy run alignment mafft_add '$inputs'</command>
23 <configfiles> 23 <configfiles>
24 <inputs name="inputs" data_style="staging_path_and_source_path"/> 24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
38 </param> 38 </param>
39 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 39 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
40 <param name="parttree" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parttree: Bool" help="[default: No] This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default"/> 40 <param name="parttree" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parttree: Bool" help="[default: No] This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default"/>
41 <param name="addfragments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="addfragments: Bool" help="[default: No] Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used."/> 41 <param name="addfragments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="addfragments: Bool" help="[default: No] Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used."/>
42 <param name="keeplength" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="keeplength: Bool" help="[default: No] If selected, the alignment length will be unchanged. Any added sequence that would otherwise introduce new insertions into the alignment, will have those insertions deleted, to preserve original alignment length."/> 42 <param name="keeplength" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="keeplength: Bool" help="[default: No] If selected, the alignment length will be unchanged. Any added sequence that would otherwise introduce new insertions into the alignment, will have those insertions deleted, to preserve original alignment length."/>
43 <param name="large" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="large: Bool" help="[default: No] This flag is required when aligning very large datasets that do not otherwise fit into memory. Temporary data is then stored in files, instead of RAM. The --use-cache flag specifies the storage location of the temporary files created. By default, $TMP/qiime2/ is used."/>
43 </section> 44 </section>
44 </inputs> 45 </inputs>
45 <outputs> 46 <outputs>
46 <data name="expanded_alignment" format="qza" label="${tool.name} on ${on_string}: expanded_alignment.qza" from_work_dir="expanded_alignment.qza"/> 47 <data name="expanded_alignment" format="qza" label="${tool.name} on ${on_string}: expanded_alignment.qza" from_work_dir="expanded_alignment.qza"/>
47 </outputs> 48 </outputs>