diff filtlong.xml @ 3:41b2ad601cf0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"

--- a/filtlong.xml	Wed Mar 31 08:19:02 2021 +0000
+++ b/filtlong.xml	Thu Feb 24 21:22:16 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="filtlong" name="filtlong" version="@WRAPPER_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="filtlong" name="filtlong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Filtering long reads by quality</description>
     <macros>
         <import>macros.xml</import>
@@ -22,6 +22,9 @@
     #if $output_thresholds.min_window_q:
         --min_window_q '$output_thresholds.min_window_q'
     #end if
+    #if $output_thresholds.max_length:
+        --max_length '$output_thresholds.max_length' 
+    #end if
     #if $external_references.assembly:
         --assembly '$external_references.assembly'
     #end if
@@ -48,6 +51,7 @@
         <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="--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="--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"/>
@@ -93,6 +97,11 @@
             <param name="split" value="500"/>
             <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/>
         </test>
+        <test>
+            <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
+            <param name="max_length" value="5000"/>
+            <output name="outfile" ftype="fastqsanger" file="output_max_length.fastq"/>
+        </test>
     </tests>
     <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.