# HG changeset patch
# User devteam
# Date 1506794169 14400
# Node ID 4844c1810c16384fc2831591816d5ecd8f9db240
# Parent  723b5b38d88a484794de3593e1acc57bc1fbc3e6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a

diff -r 723b5b38d88a -r 4844c1810c16 fastq_to_fasta.py
--- a/fastq_to_fasta.py	Wed Nov 11 12:43:11 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-#Dan Blankenberg
-import sys
-from galaxy_utils.sequence.fastq import fastqReader
-from galaxy_utils.sequence.fasta import fastaWriter
-
-def main():
-    input_filename = sys.argv[1]
-    output_filename = sys.argv[2]
-    input_type = sys.argv[3] or 'sanger' #input type should ordinarily be unnecessary
-    
-    num_reads = None
-    fastq_read = None
-    out = fastaWriter( open( output_filename, 'wb' ) )
-    for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
-        out.write( fastq_read )
-    out.close()
-    if num_reads is None:
-        print "No valid FASTQ reads could be processed."
-    else:
-        print "%i FASTQ reads were converted to FASTA." % ( num_reads + 1 )
-    
-if __name__ == "__main__": main()
diff -r 723b5b38d88a -r 4844c1810c16 fastq_to_fasta.xml
--- a/fastq_to_fasta.xml	Wed Nov 11 12:43:11 2015 -0500
+++ b/fastq_to_fasta.xml	Sat Sep 30 13:56:09 2017 -0400
@@ -1,42 +1,40 @@
-<tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.0.0">
-  <description>converter</description>
-  <requirements>
-    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
-  </requirements>
-  <command interpreter="python">fastq_to_fasta.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command>
-  <inputs>
-    <param name="input_file" type="data" format="fastq" label="FASTQ file to convert" />
-  </inputs>
-  <outputs>
-    <data name="output_file" format="fasta" />
-  </outputs>
-  <tests>
-    <!-- basic test -->
-    <test>
-      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-      <output name="output_file" file="fastq_to_fasta_python_1.out" />
-    </test>
-    <!-- color space test -->
-    <test>
-      <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
-      <output name="output_file" file="fastq_to_fasta_python_2.out" />
-    </test>
-    <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
-    <test>
-      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
-      <output name="output_file" file="fastq_to_fasta_python_1.out" />
-    </test>
-  </tests>
-  <help>
+<tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.1.1">
+    <description>converter</description>
+    <requirements>
+        <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
+    </requirements>
+    <command><![CDATA[
+gx-fastq-to-fasta '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}'
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2" label="FASTQ file to convert" />
+    </inputs>
+    <outputs>
+        <data name="output_file" format="fasta" />
+    </outputs>
+    <tests>
+        <!-- basic test -->
+        <test>
+            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+            <output name="output_file" file="fastq_to_fasta_python_1.out" />
+        </test>
+        <!-- color space test -->
+        <test>
+            <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
+            <output name="output_file" file="fastq_to_fasta_python_2.out" />
+        </test>
+        <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
+        <test>
+            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
+            <output name="output_file" file="fastq_to_fasta_python_1.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 This tool converts FASTQ sequencing reads to FASTA sequences.
-
-
-  </help>
-  
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq281</citation>
-  </citations>
-  
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq281</citation>
+    </citations>
 </tool>
diff -r 723b5b38d88a -r 4844c1810c16 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 11 12:43:11 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="galaxy_sequence_utils" version="1.0.0">
-      <repository changeset_revision="0643676ad5f7" name="package_galaxy_utils_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>