changeset 5:1dfbdcbf604b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong commit 9981466001b7c3e7efa68bcb84337b76ad290da3

--- a/filtlong.xml	Wed Nov 01 08:35:30 2023 +0000
+++ b/filtlong.xml	Mon Aug 18 12:38:23 2025 +0000
@@ -29,11 +29,11 @@
     #if $external_references.assembly:
         --assembly '$external_references.assembly'
     #end if
-    #if $external_references.illumina_1:
-        --illumina_1 '$external_references.illumina_1'
+    #if $external_references.short_1:
+        --short_1 '$external_references.short_1'
     #end if
-    #if $external_references.illumina_2:
-        --illumina_2 '$external_references.illumina_2'
+    #if $external_references.short_2:
+        --short_2 '$external_references.short_2'
     #end if
     --length_weight '$score_weights.length_weight'
     --mean_q_weight '$score_weights.mean_q_weight'
@@ -59,8 +59,8 @@
         </section>
         <section name="external_references" title="External references">
             <param argument="--assembly" type="data" format="fasta,fasta.gz" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
-            <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
-            <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
+            <param argument="--short_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
+            <param argument="--short_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
         </section>
         <section name="score_weights" title="Score weights">
             <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/>
@@ -79,28 +79,38 @@
         <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
-            <param name="min_length" value="1000"/>
-            <param name="keep_percent" value="50"/>
-            <param name="target_bases" value="500000000"/>
+            <section name="output_thresholds">
+                <param name="min_length" value="1000"/>
+                <param name="keep_percent" value="50"/>
+                <param name="target_bases" value="500000000"/>
+            </section>
             <output name="outfile" ftype="fastqsanger" file="output.fastq"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
-            <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/>
-            <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/>
-            <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/>
-            <param name="min_length" value="1000"/>
-            <param name="keep_percent" value="90"/>
-            <param name="target_bases" value="500000000"/>
-            <param name="trim" value="True"/>
-            <param name="split" value="500"/>
+            <section name="external_references">
+                <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/>
+                <param name="short_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/>
+                <param name="short_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/>
+            </section>
+            <section name="output_thresholds">
+                <param name="min_length" value="1000"/>
+                <param name="keep_percent" value="90"/>
+                <param name="target_bases" value="500000000"/>
+            </section>
+            <section name="read_manipulation">
+                <param name="trim" value="True"/>
+                <param name="split" value="500"/>
+            </section>
             <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
-            <param name="max_length" value="5000"/>
+            <section name="output_thresholds">
+                <param name="max_length" value="5000"/>
+            </section>
             <output name="outfile" ftype="fastqsanger" file="output_max_length.fastq"/>
         </test>
     </tests>

--- a/macros.xml	Wed Nov 01 08:35:30 2023 +0000
+++ b/macros.xml	Mon Aug 18 12:38:23 2025 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.2.1</token>
+    <token name="@TOOL_VERSION@">0.3.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="biotools">