Mercurial > repos > q2d2 > qiime2__alignment__mask

annotate qiime2__alignment__mask.xml @ 2:e8bee857dc0d 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__alignment commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:34:03 +0000
parents 58797be8efd4
children dd189714b70d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
1 <?xml version='1.0' encoding='utf-8'?>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
2 <!--
1
58797be8efd4 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
3 Copyright (c) 2023, QIIME 2 development team.
0
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
4
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
6 -->
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
7 <!--
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
8 This tool was automatically generated by:
2
e8bee857dc0d planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 65e4952f33eb335528e8553150e9097e5ea8f556
q2d2
parents: 1
diff changeset
9 q2galaxy (version: 2023.5.0)
0
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
10 for:
2
e8bee857dc0d planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 65e4952f33eb335528e8553150e9097e5ea8f556
q2d2
parents: 1
diff changeset
11 qiime2 (version: 2023.5.1)
0
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
12 -->
2
e8bee857dc0d planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 65e4952f33eb335528e8553150e9097e5ea8f556
q2d2
parents: 1
diff changeset
13 <tool name="qiime2 alignment mask" id="qiime2__alignment__mask" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
0
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
14 <description>Positional conservation and gap filtering.</description>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
15 <requirements>
2
e8bee857dc0d planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 65e4952f33eb335528e8553150e9097e5ea8f556
q2d2
parents: 1
diff changeset
16 <container type="docker">quay.io/qiime2/core:2023.5</container>
0
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
17 </requirements>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
18 <version_command>q2galaxy version alignment</version_command>
1
58797be8efd4 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 69da7976573cc07a363ac66bdacc9269d7cd3732
q2d2
parents: 0
diff changeset
19 <command detect_errors="exit_code">q2galaxy run alignment mask '$inputs'</command>
0
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
20 <configfiles>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
21 <inputs name="inputs" data_style="paths"/>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
22 </configfiles>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
23 <inputs>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
24 <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required] The alignment to be masked.">
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
25 <options options_filter_attribute="metadata.semantic_type">
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
26 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
27 </options>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
29 </param>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
31 <param name="max_gap_frequency" type="float" min="0" max="1" value="1.0" label="max_gap_frequency: Float % Range(0, 1, inclusive_end=True)" help="[default: 1.0] The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency."/>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
32 <param name="min_conservation" type="float" min="0" max="1" value="0.4" label="min_conservation: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.4] The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences."/>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
33 </section>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
34 </inputs>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
35 <outputs>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
36 <data name="masked_alignment" format="qza" label="${tool.name} on ${on_string}: masked_alignment.qza" from_work_dir="masked_alignment.qza"/>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
37 </outputs>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
38 <tests/>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
39 <help>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
40 QIIME 2: alignment mask
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
41 =======================
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
42 Positional conservation and gap filtering.
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
43
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
44
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
45 Outputs:
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
46 --------
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
47 :masked_alignment.qza: The masked alignment.
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
48
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
49 |
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
50
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
51 Description:
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
52 ------------
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
53 Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
54
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
55
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
56 |
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
57
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
58 </help>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
59 <citations>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
60 <citation type="bibtex">@incollection{cite1,
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
61 address = {New York},
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
62 author = {Lane, DJ},
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
63 booktitle = {Nucleic Acid Techniques in Bacterial Systematics},
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
64 editor = {Stackebrandt, E and Goodfellow, M},
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
65 pages = {115--175},
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
66 publisher = {John Wiley and Sons},
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
67 title = {16S/23S rRNA sequencing},
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
68 year = {1991}
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
69 }
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
70 </citation>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
71 <citation type="doi">10.1038/s41587-019-0209-9</citation>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
72 </citations>
610253dfe672 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff changeset
73 </tool>