changeset 2:8d441435b9e6 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7

--- a/qiime2__rescript__extract_seq_segments.xml	Mon Jun 03 23:31:04 2024 +0000
+++ b/qiime2__rescript__extract_seq_segments.xml	Wed Oct 30 19:55:12 2024 +0000
@@ -6,14 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<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">
+<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">
     <description>Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version rescript</version_command>
     <command detect_errors="exit_code">q2galaxy run rescript extract_seq_segments '$inputs'</command>
@@ -27,7 +30,7 @@
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
         </param>
-        <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'.">
+        <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'.">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureData[Sequence]"/>
             </options>
@@ -35,6 +38,7 @@
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
             <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."/>
+            <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'."/>
             <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."/>
             <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."/>
         </section>