# HG changeset patch
# User iuc
# Date 1758645190 0
# Node ID 0d9cd7b02f1423f7e29118390c3ff93adeb2499a
# Parent  1dfbdcbf604b048000ae31dca5d1826a8fa641f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong commit 5875d08292df3ceac45962dcc1790a36de9dcf9a

diff -r 1dfbdcbf604b -r 0d9cd7b02f14 filtlong.xml
--- a/filtlong.xml	Mon Aug 18 12:38:23 2025 +0000
+++ b/filtlong.xml	Tue Sep 23 16:33:10 2025 +0000
@@ -50,10 +50,16 @@
     <inputs>
         <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ" help="FASTQ of input reads"/>
         <section name="output_thresholds" title="Output thresholds">
-            <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/>
+            <param argument="--target_bases" type="text" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases (unit suffixes: k, kb, m, mb, g, gb).">
+                <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
+            </param>
             <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/>
-            <param argument="--max_length" type="integer" min="0" optional="True" label="Max. length" help="Maximum length threshold"/>
-            <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/>
+            <param argument="--max_length" type="text" min="0" optional="True" label="Max. length" help="Maximum length threshold (unit suffixes: k, kb, m, mb, g, gb)">
+                <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
+            </param>
+            <param argument="--min_length" type="text" min="0" optional="True" label="Min. length" help="Minimum length threshold (unit suffixes: k, kb, m, mb, g, gb)">
+                <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
+            </param>
             <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/>
             <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
         </section>
@@ -69,7 +75,9 @@
         </section>
         <section name="read_manipulation" title="Read manipulation">
             <param argument="--trim" type="boolean" checked="false" truevalue="--trim" falsevalue="" label="Trim non-k-mer-matching" help="Trim non-k-mer-matching bases from start/end of reads"/>
-            <param argument="--split" type="integer" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases"/>
+            <param argument="--split" type="text" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases">
+                <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
+            </param>
         </section>
         <section name="other" title="Other">
             <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/>
@@ -84,7 +92,7 @@
             <section name="output_thresholds">
                 <param name="min_length" value="1000"/>
                 <param name="keep_percent" value="50"/>
-                <param name="target_bases" value="500000000"/>
+                <param name="target_bases" value="500mb"/>
             </section>
             <output name="outfile" ftype="fastqsanger" file="output.fastq"/>
         </test>
@@ -98,7 +106,7 @@
             <section name="output_thresholds">
                 <param name="min_length" value="1000"/>
                 <param name="keep_percent" value="90"/>
-                <param name="target_bases" value="500000000"/>
+                <param name="target_bases" value="500mb"/>
             </section>
             <section name="read_manipulation">
                 <param name="trim" value="True"/>
@@ -117,16 +125,5 @@
     <help><![CDATA[
 Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
     ]]></help>
-    <citations>
-        <citation type="bibtex">
-            @misc{rrwick2017,
-                author = {Wick, Ryan},
-                year = {2017},
-                title = {Filtlong},
-                publisher = {GitHub},
-                journal = {GitHub repository},
-                url = {https://github.com/rrwick/Filtlong},
-            }
-        </citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>
diff -r 1dfbdcbf604b -r 0d9cd7b02f14 macros.xml
--- a/macros.xml	Mon Aug 18 12:38:23 2025 +0000
+++ b/macros.xml	Tue Sep 23 16:33:10 2025 +0000
@@ -1,12 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.3.0</token>
+    <token name="@TOOL_VERSION@">0.3.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="biotools">
         <xrefs>
-            <xref type="bio.tools">
-                filtlong
-            </xref>
+            <xref type="bio.tools">filtlong</xref>
         </xrefs>
     </xml>
     <xml name="requirements">
@@ -14,5 +12,18 @@
             <requirement type="package" version="@TOOL_VERSION@">filtlong</requirement>
         </requirements>
     </xml>
-</macros>
-
+     <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{rrwick2017,
+                    author = {Wick, Ryan},
+                    year = {2017},
+                    title = {Filtlong},
+                    publisher = {GitHub},
+                    journal = {GitHub repository},
+                    url = {https://github.com/rrwick/Filtlong},
+                }
+            </citation>
+        </citations>
+    </xml>
+</macros>
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