Mercurial > repos > p.lucas > fasta_to_fastq

changeset 2:1ae786d82161 draft

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Uploaded
author p.lucas
date Wed, 24 Jul 2024 12:44:39 +0000
parents 60e768cf5101
children 2f317786c4e7
files fasta_to_fastq.xml
diffstat 1 files changed, 10 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/fasta_to_fastq.xml	Tue Jul 23 14:28:53 2024 +0000
+++ b/fasta_to_fastq.xml	Wed Jul 24 12:44:39 2024 +0000
@@ -1,23 +1,26 @@
-<tool id="fasta_to_fastq" name="FASTA to FASTQ" version="1.0">
+<tool id="fasta_to_fastq" name="FASTA to FASTQ" version="1.1">
   <description>Convert a FASTA file to a FASTQ file</description>
   <requirements>
     <requirement type="package" version="1.79">biopython</requirement>
   </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
   <command><![CDATA[
     python '$__tool_directory__/fasta2fastq.py' 
-      -i "$inputfile"
-      -s "$score"
-      -o "$output"
+      -i "$inputfile" 
+      -s "$score" 
+      -o "$output" 
   ]]>
   </command>
   <inputs>
     <param type="data" name="inputfile" format="fasta" label="Input fasta file"/>
-    <param type="integer" name="score" label="Quality score" value="40" help="Quality score you wanted for each base in all reads. (default: 40)"/>
+    <param type="integer" name="score" label="Quality score (only positive int)" value="40"/>
   </inputs>
   <outputs>
-    <data name="output" format="fastq" label="${tool.name} on ${on_string}"/>
+    <data name="output" format="fastq"/>
   </outputs>
-  <help> <![CDATA[
+  <help><![CDATA[
     Takes a FASTA file and converts it to a FASTQ file by adding a static quality score. The default quality score for each base in all reads is 40.
   ]]> 
   </help>