diff fastq_to_fasta.xml @ 0:3571553aeb20 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_to_fasta.xml	Mon Jan 27 09:27:22 2014 -0500
@@ -0,0 +1,43 @@
+<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>
+**What it does**
+
+This tool converts FASTQ sequencing reads to FASTA sequences.
+
+------
+
+**Citation**
+
+If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
+
+
+  </help>
+</tool>