Mercurial > repos > q2d2 > qiime2__rescript__extract_seq_segments

comparison qiime2__rescript__extract_seq_segments.xml @ 2:8d441435b9e6 draft default tip

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 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:55:12 +0000
parents 555ba9f92313
children
comparison
equal deleted inserted replaced
1:555ba9f92313 2:8d441435b9e6
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 rescript extract-seq-segments" id="qiime2__rescript__extract_seq_segments" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 rescript extract-seq-segments" id="qiime2__rescript__extract_seq_segments" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
14 <description>Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value.</description> 14 <description>Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value.</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 rescript</version_command> 21 <version_command>q2galaxy version rescript</version_command>
19 <command detect_errors="exit_code">q2galaxy run rescript extract_seq_segments '$inputs'</command> 22 <command detect_errors="exit_code">q2galaxy run rescript extract_seq_segments '$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"/>
25 <options options_filter_attribute="metadata.semantic_type"> 28 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureData[Sequence]"/> 29 <filter type="add_value" value="FeatureData[Sequence]"/>
27 </options> 30 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> 31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
29 </param> 32 </param>
30 <param name="reference_segment_sequences" type="data" format="qza" label="reference_segment_sequences: FeatureData[Sequence]" help="[required] Reference sequence segments that will be used to search for and extract matching segments from 'sequences'."> 33 <param name="reference_segment_sequences" type="data" format="qza" label="reference_segment_sequences: FeatureData[Sequence]" help="[required] Reference sequence segments that will be used to search for and extract matching segments from 'input-sequences'.">
31 <options options_filter_attribute="metadata.semantic_type"> 34 <options options_filter_attribute="metadata.semantic_type">
32 <filter type="add_value" value="FeatureData[Sequence]"/> 35 <filter type="add_value" value="FeatureData[Sequence]"/>
33 </options> 36 </options>
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="perc_identity" type="float" min="1e-06" max="1" value="0.7" label="perc_identity: Float % Range(0, 1, inclusive_start=False, inclusive_end=True)" help="[default: 0.7] The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter."/> 40 <param name="perc_identity" type="float" min="1e-06" max="1" value="0.7" label="perc_identity: Float % Range(0, 1, inclusive_start=False, inclusive_end=True)" help="[default: 0.7] The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter."/>
41 <param name="target_coverage" type="float" min="1e-06" max="1" value="0.9" label="target_coverage: Float % Range(0, 1, inclusive_start=False, inclusive_end=True)" help="[default: 0.9] The minimum fraction of coverage that 'reference-segment-sequences' must have in order to extract matching segments from 'input-sequences'."/>
38 <param name="min_seq_len" type="integer" min="1" optional="true" label="min_seq_len: Int % Range(1, None)" help="[optional] Minimum length of sequence allowed for searching. Any sequence less than this will be discarded. If not set, default program settings will be used."/> 42 <param name="min_seq_len" type="integer" min="1" optional="true" label="min_seq_len: Int % Range(1, None)" help="[optional] Minimum length of sequence allowed for searching. Any sequence less than this will be discarded. If not set, default program settings will be used."/>
39 <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."/> 43 <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."/>
40 </section> 44 </section>
41 </inputs> 45 </inputs>
42 <outputs> 46 <outputs>