Mercurial > repos > q2d2 > qiime2__quality_control__decontam_remove

changeset 2:ceb8db9c0509 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit c7e80dcda727ce63b42aa8a946e9330310929797
author q2d2
date Mon, 03 Jun 2024 23:30:21 +0000
parents 9edda646c9dd
children 239447c3062a
files qiime2__quality_control__decontam_remove.xml
diffstat 1 files changed, 19 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__quality_control__decontam_remove.xml	Thu Apr 25 21:18:15 2024 +0000
+++ b/qiime2__quality_control__decontam_remove.xml	Mon Jun 03 23:30:21 2024 +0000
@@ -6,14 +6,14 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 quality-control decontam-remove" id="qiime2__quality_control__decontam_remove" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
-    <description>Removes contaminant</description>
+<tool name="qiime2 quality-control decontam-remove" id="qiime2__quality_control__decontam_remove" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+    <description>Remove contaminants</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version quality_control</version_command>
     <command detect_errors="exit_code">q2galaxy run quality_control decontam_remove '$inputs'</command>
@@ -21,41 +21,49 @@
         <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
-        <param name="decontam_scores" type="data" format="qza" label="decontam_scores: FeatureData[DecontamScore]" help="[required]  Output table from decontam identify">
+        <param name="decontam_scores" type="data" format="qza" label="decontam_scores: FeatureData[DecontamScore]" help="[required]  Pre-feature decontam scores.">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureData[DecontamScore]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DecontamScore]']</validator>
         </param>
-        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  ASV or OTU table which contaminate sequences will be identified from">
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  Feature table from which contaminants will be removed.">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
         </param>
+        <param name="rep_seqs" type="data" format="qza" label="rep_seqs: FeatureData[Sequence]" help="[required]  Feature representative sequences from which contaminants will be removed.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Sequence]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
+        </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
-            <param name="threshold" type="float" value="0.1" label="threshold: Float" help="[default: 0.1]  Select threshold cutoff for decontam algorithm scores"/>
+            <param name="threshold" type="float" min="0.0" max="1.0" value="0.1" label="threshold: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.1]  Decontam score threshold. Features with a score less than or equal to this threshold will be removed."/>
         </section>
     </inputs>
     <outputs>
         <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
+        <data name="filtered_rep_seqs" format="qza" label="${tool.name} on ${on_string}: filtered_rep_seqs.qza" from_work_dir="filtered_rep_seqs.qza"/>
     </outputs>
     <tests/>
     <help>
 QIIME 2: quality-control decontam-remove
 ========================================
-Removes contaminant
+Remove contaminants
 
 
 Outputs:
 --------
-:filtered_table.qza: The resulting feature table of scores once contaminants are removed
+:filtered_table.qza: Feature table with contaminants removed.
+:filtered_rep_seqs.qza: Feature representative sequences with contaminants removed.
 
 |  
 
 Description:
 ------------
-This method removes contaminant sequences from an OTU or ASV table and returns the amended table to the user
+Remove contaminant sequences from a feature table and the associated representative sequences.
 
 
 |