Mercurial > repos > iuc > filtlong

diff filtlong.xml @ 2:a72af9de6bf5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
author iuc
date Wed, 31 Mar 2021 08:19:02 +0000
parents 8880fb74ef56
children 41b2ad601cf0
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--- a/filtlong.xml	Wed Sep 19 08:21:21 2018 -0400
+++ b/filtlong.xml	Wed Mar 31 08:19:02 2021 +0000
@@ -1,8 +1,9 @@
-<tool id="filtlong" name="filtlong" version="0.2.0">
+<tool id="filtlong" name="filtlong" version="@WRAPPER_VERSION@+galaxy1" profile="@PROFILE@">
     <description>Filtering long reads by quality</description>
-    <requirements>
-        <requirement type="package" version="0.2.0">filtlong</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <version_command>filtlong --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
 filtlong
@@ -43,7 +44,7 @@
     '$input_file' > output.fastq
     ]]></command>
     <inputs>
-        <param name="input_file" type="data" format="fastqsanger" label="Input FASTQ" help="FASTQ of input reads"/>
+        <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="--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)"/>
@@ -52,7 +53,7 @@
             <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
         </section>
         <section name="external_references" title="External references">
-            <param argument="--assembly" type="data" format="fasta" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
+            <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"/>
         </section>
@@ -74,14 +75,15 @@
     </outputs>
     <tests>
         <test>
-            <param name="input_file" ftype="fastqsanger" value="test.fastq"/>
+            <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"/>
             <output name="outfile" ftype="fastqsanger" file="output.fastq"/>
         </test>
         <test>
-            <param name="input_file" ftype="fastqsanger" value="test_reference.fasta"/>
+            <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"/>