Mercurial > repos > q2d2 > qiime2__rescript__trim_alignment

changeset 2:8659a1689f71 draft default tip

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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 19:55:36 +0000
parents f14be3f75d11
children
files qiime2__rescript__trim_alignment.xml
diffstat 1 files changed, 10 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__rescript__trim_alignment.xml	Mon Jun 03 23:31:13 2024 +0000
+++ b/qiime2__rescript__trim_alignment.xml	Wed Oct 30 19:55:36 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 trim-alignment" id="qiime2__rescript__trim_alignment" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 rescript trim-alignment" id="qiime2__rescript__trim_alignment" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Trim alignment based on provided primers or specific positions.</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 trim_alignment '$inputs'</command>
@@ -29,7 +32,7 @@
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
             <conditional name="__q2galaxy__GUI__conditional__primer_fwd__" label="primer_fwd: Str">
-                <param name="__q2galaxy__GUI__select__" type="select" label="primer_fwd: Str" help="[optional]  Forward primer used to find the start position for alignment trimming.">
+                <param name="__q2galaxy__GUI__select__" type="select" label="primer_fwd: Str" help="[optional]  Forward primer used to find the start position for alignment trimming. Provide as 5'-3'.">
                     <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
                     <option value="__q2galaxy__::control::provide">Provide a value</option>
                 </param>
@@ -45,7 +48,7 @@
                 </when>
             </conditional>
             <conditional name="__q2galaxy__GUI__conditional__primer_rev__" label="primer_rev: Str">
-                <param name="__q2galaxy__GUI__select__" type="select" label="primer_rev: Str" help="[optional]  Reverse primer used to find the end position for alignment trimming.">
+                <param name="__q2galaxy__GUI__select__" type="select" label="primer_rev: Str" help="[optional]  Reverse primer used to find the end position for alignment trimming. Provide as 5'-3'.">
                     <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
                     <option value="__q2galaxy__::control::provide">Provide a value</option>
                 </param>
@@ -62,6 +65,7 @@
             </conditional>
             <param name="position_start" type="integer" min="1" optional="true" label="position_start: Int % Range(1, None)" help="[optional]  Position within the alignment where the trimming will begin. If not provided, alignment will notbe trimmed at the beginning. If forward primer isspecified this parameter will be ignored."/>
             <param name="position_end" type="integer" min="1" optional="true" label="position_end: Int % Range(1, None)" help="[optional]  Position within the alignment where the trimming will end. If not provided, alignment will not be trimmed at the end. If reverse primer is specified this parameter will be ignored."/>
+            <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1]  Number of threads to use for primer-based trimming, otherwise ignored. (Use `auto` to automatically use all available cores)"/>
         </section>
     </inputs>
     <outputs>