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comparison qiime2__alignment__mafft_add.xml @ 5:793348b25298 draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:35:56 +0000
parents 51e7e9d2c302
children
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4:51e7e9d2c302 5:793348b25298
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: 2024.5.0) 9 q2galaxy (version: 2024.10.0)
10 for: 10 for:
11 qiime2 (version: 2024.5.0) 11 qiime2 (version: 2024.10.1)
12 --> 12 -->
13 <tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2024.10.0+q2galaxy.2024.10.0" 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>
16 <xref type="bio.tools">qiime2</xref>
17 </xrefs>
15 <requirements> 18 <requirements>
16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container> 19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
17 </requirements> 20 </requirements>
18 <version_command>q2galaxy version alignment</version_command> 21 <version_command>q2galaxy version alignment</version_command>
19 <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>
20 <configfiles> 23 <configfiles>
21 <inputs name="inputs" data_style="staging_path_and_source_path"/> 24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> 37 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
35 </param> 38 </param>
36 <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">
37 <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"/>
38 <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."/>
39 </section> 43 </section>
40 </inputs> 44 </inputs>
41 <outputs> 45 <outputs>
42 <data name="expanded_alignment" format="qza" label="${tool.name} on ${on_string}: expanded_alignment.qza" from_work_dir="expanded_alignment.qza"/> 46 <data name="expanded_alignment" format="qza" label="${tool.name} on ${on_string}: expanded_alignment.qza" from_work_dir="expanded_alignment.qza"/>
43 </outputs> 47 </outputs>