comparison qiime2__phylogeny__align_to_tree_mafft_fasttree.xml @ 1:43e5dd36de74 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 69da7976573cc07a363ac66bdacc9269d7cd3732

0:fd05e62ba9f9

<?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 phylogeny align-to-tree-mafft-fasttree" id="qiime2__phylogeny__align_to_tree_mafft_fasttree" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Build a phylogenetic tree using fasttree and mafft alignment</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version phylogeny</version_command>
    <command detect_errors="aggressive">q2galaxy run phylogeny align_to_tree_mafft_fasttree '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  The sequences to be used for creating a fasttree based rooted phylogenetic tree.">

        <data name="alignment" format="qza" label="${tool.name} on ${on_string}: alignment.qza" from_work_dir="alignment.qza"/>
        <data name="masked_alignment" format="qza" label="${tool.name} on ${on_string}: masked_alignment.qza" from_work_dir="masked_alignment.qza"/>
        <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>
        <data name="rooted_tree" format="qza" label="${tool.name} on ${on_string}: rooted_tree.qza" from_work_dir="rooted_tree.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: phylogeny align-to-tree-mafft-fasttree
===============================================
Build a phylogenetic tree using fasttree and mafft alignment

Description:
------------
This pipeline will start by creating a sequence alignment using MAFFT, after which any alignment columns that are phylogenetically uninformative or ambiguously aligned will be removed (masked). The resulting masked alignment will be used to infer a phylogenetic tree and then subsequently rooted at its midpoint. Output files from each step of the pipeline will be saved. This includes both the unmasked and masked MAFFT alignment from q2-alignment methods, and both the rooted and unrooted phylogenies from q2-phylogeny methods.


|  

</help>
    <citations>

1:43e5dd36de74

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2023, 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: 2022.11.1)
for:
    qiime2 (version: 2022.11.1)
-->
<tool name="qiime2 phylogeny align-to-tree-mafft-fasttree" id="qiime2__phylogeny__align_to_tree_mafft_fasttree" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Build a phylogenetic tree using fasttree and mafft alignment</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version phylogeny</version_command>
    <command detect_errors="exit_code">q2galaxy run phylogeny align_to_tree_mafft_fasttree '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  The sequences to be used for creating a fasttree based rooted phylogenetic tree.">

        <data name="alignment" format="qza" label="${tool.name} on ${on_string}: alignment.qza" from_work_dir="alignment.qza"/>
        <data name="masked_alignment" format="qza" label="${tool.name} on ${on_string}: masked_alignment.qza" from_work_dir="masked_alignment.qza"/>
        <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>
        <data name="rooted_tree" format="qza" label="${tool.name} on ${on_string}: rooted_tree.qza" from_work_dir="rooted_tree.qza"/>
    </outputs>
    <tests>
        <test>
            <param name="sequences" value="align_to_tree_mafft_fasttree.test0.rep-seqs.qza" ftype="qza"/>
            <output name="alignment" ftype="qza">
                <assert_contents>
                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
                        <has_line_matching expression="type: FeatureData\[AlignedSequence\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
            <output name="masked_alignment" ftype="qza">
                <assert_contents>
                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
                        <has_line_matching expression="type: FeatureData\[AlignedSequence\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
            <output name="tree" ftype="qza">
                <assert_contents>
                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
                        <has_line_matching expression="type: Phylogeny\[Unrooted\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
            <output name="rooted_tree" ftype="qza">
                <assert_contents>
                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
                        <has_line_matching expression="type: Phylogeny\[Rooted\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
QIIME 2: phylogeny align-to-tree-mafft-fasttree
===============================================
Build a phylogenetic tree using fasttree and mafft alignment

Description:
------------
This pipeline will start by creating a sequence alignment using MAFFT, after which any alignment columns that are phylogenetically uninformative or ambiguously aligned will be removed (masked). The resulting masked alignment will be used to infer a phylogenetic tree and then subsequently rooted at its midpoint. Output files from each step of the pipeline will be saved. This includes both the unmasked and masked MAFFT alignment from q2-alignment methods, and both the rooted and unrooted phylogenies from q2-phylogeny methods.

Examples:
---------

align_to_tree_mafft_fasttree
****************************
Using the ``qiime2 phylogeny align-to-tree-mafft-fasttree`` tool:
 #. Set *"sequences"* to ``#: rep-seqs.qza``
 #. Press the ``Execute`` button.

Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows:
 (Renaming is optional, but it will make any subsequent steps easier to complete.)

 .. list-table::
    :align: left
    :header-rows: 1

    * - History Name
      - *"Name"* to set (be sure to press ``Save``)
    * - ``#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : alignment.qza``
      - ``aligned-rep-seqs.qza``
    * - ``#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : masked_alignment.qza``
      - ``masked-aligned-rep-seqs.qza``
    * - ``#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : tree.qza``
      - ``unrooted-tree.qza``
    * - ``#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : rooted_tree.qza``
      - ``rooted-tree.qza``


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</help>
    <citations>