# HG changeset patch
# User q2d2
# Date 1762017069 0
# Node ID 4c13a2d68a2a7e5f6d6a4b449e0291f7353c1060
# Parent  e3d4217c9a64bf2e29e7b6822d5d287b27086155
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

diff -r e3d4217c9a64 -r 4c13a2d68a2a qiime2__demux__filter_samples.xml
--- a/qiime2__demux__filter_samples.xml	Tue Jul 15 21:49:18 2025 +0000
+++ b/qiime2__demux__filter_samples.xml	Sat Nov 01 17:11:09 2025 +0000
@@ -6,17 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2025.7.0)
+    q2galaxy (version: 2025.10.0)
 for:
-    qiime2 (version: 2025.7.0)
+    qiime2 (version: 2025.10.0)
 -->
-<tool name="qiime2 demux filter-samples" id="qiime2__demux__filter_samples" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 demux filter-samples" id="qiime2__demux__filter_samples" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Filter samples out of demultiplexed data.</description>
     <xrefs>
         <xref type="bio.tools">qiime2</xref>
     </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2025.7</container>
+        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
     </requirements>
     <version_command>q2galaxy version demux</version_command>
     <command detect_errors="exit_code">q2galaxy run demux filter_samples '$inputs'</command>
@@ -26,27 +26,27 @@
     <inputs>
         <param name="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]" help="[required]  The demultiplexed data from which samples should be filtered.">
             <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
-                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
         </param>
-        <repeat name="metadata" min="1" help="[required]  Sample metadata indicating which sample ids to filter. The optional `where` parameter may be used to filter ids based on specified conditions in the metadata. The optional `exclude_ids` parameter may be used to exclude the ids specified in the metadata from the filter." title="metadata: Metadata">
-            <conditional name="__q2galaxy__GUI__conditional__metadata__">
-                <param name="type" type="select" label="metadata: Metadata">
-                    <option value="tsv" selected="true">Metadata from TSV</option>
-                    <option value="qza">Metadata from Artifact</option>
-                </param>
-                <when value="tsv">
-                    <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
-                </when>
-                <when value="qza">
-                    <param name="source" type="data" format="qza" label="Metadata Source"/>
-                </when>
-            </conditional>
-        </repeat>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <repeat name="metadata" help="[optional]  Sample metadata indicating which sample ids to filter. The optional `where` parameter may be used to filter ids based on specified conditions in the metadata. The optional `exclude_ids` parameter may be used to exclude the ids specified in the metadata from the filter." title="metadata: Metadata">
+                <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                    <param name="type" type="select" label="metadata: Metadata">
+                        <option value="tsv" selected="true">Metadata from TSV</option>
+                        <option value="qza">Metadata from Artifact</option>
+                    </param>
+                    <when value="tsv">
+                        <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
+                    </when>
+                    <when value="qza">
+                        <param name="source" type="data" format="qza" label="Metadata Source"/>
+                    </when>
+                </conditional>
+            </repeat>
             <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str">
                 <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional]  Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained.">
                     <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
@@ -64,6 +64,7 @@
                 </when>
             </conditional>
             <param name="exclude_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="exclude_ids: Bool" help="[default: No]  Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data."/>
+            <param name="remove_empty" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="remove_empty: Bool" help="[default: No]  Remove samples with empty FASTQ files."/>
         </section>
     </inputs>
     <outputs>
@@ -84,7 +85,7 @@
 
 Description:
 ------------
-Filter samples indicated in given metadata out of demultiplexed data. Specific samples can be further selected with the WHERE clause, and the `exclude_ids` parameter allows for filtering of all samples not specified.
+Filter samples indicated in given metadata out of demultiplexed data or filter out empty samples. Specific samples can be further selected with the WHERE clause, and the `exclude_ids` parameter allows for filtering of all samples not specified.
 
 
 |  
diff -r e3d4217c9a64 -r 4c13a2d68a2a test-data/emp_single.test0.sequences.qza
Binary file test-data/emp_single.test0.sequences.qza has changed
diff -r e3d4217c9a64 -r 4c13a2d68a2a test-data/summarize.test0.demux.qza
Binary file test-data/summarize.test0.demux.qza has changed