# HG changeset patch
# User biowebdb
# Date 1396289435 14400
# Node ID dc29406ce9849a882bd679d574a7d3c26ddd3822
# Parent  d27bec235ad97dbf15b267c342b2f8fb03907df6
Uploaded

diff -r d27bec235ad9 -r dc29406ce984 sffextract.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sffextract.xml	Mon Mar 31 14:10:35 2014 -0400
@@ -0,0 +1,75 @@
+<tool id="biowebdb_flowgram_sffextract" name="sffextract" version="1.0.0">
+  <description>Convert SFF to FastQ or Fasta/Qual</description>
+  <requirements>
+      <requirement type="binary">sff_extract</requirement>
+  </requirements>
+  <command interpreter="ruby">sffextract.rb 
+    $input 
+    #if str( $format_options.format ) == "FASTQ"
+        $output1 
+    #else
+        $output2 $output3
+    #end if
+  </command>
+  <inputs>
+      <param name="input" type="data" format="sff" label="Input from 454 (flowgram - sff)" help="Only SFF file"/>
+      <conditional name="format_options">
+          <param name="format" type="select" label="Output format" help="">
+              <option value="FASTQ" selected="true">FastQ</option>
+              <option value="FASTA">Fasta</option>
+          </param>
+      </conditional>
+  </inputs>
+  <outputs>
+    <data name="output1" format="fastq" label="FASTQ - ${tool.name} on ${input.name}">
+        <filter>format_options['format'] == 'FASTQ'</filter>
+    </data>
+    <data name="output2" format="fasta" label="FASTA - ${tool.name} on ${input.name}">
+          <filter>format_options['format'] == 'FASTA'</filter>
+    </data>
+    <data name="output3" format="qual" label="QUAL - ${tool.name} on ${input.name}">
+        <filter>format_options['format'] == 'FASTA'</filter>
+    </data>
+  </outputs>
+  <stdio>
+    <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+    <exit_code range="1:" level="fatal"/>
+  </stdio>
+  <tests>
+    <test>
+      <!--
+      <param name="input" value="file454.sff"/>
+      <param name="format" value="FASTQ"/>
+      <output name="outfile1" file="file454.sff.fastq"/>
+      <output name="outfile1" file="file454.sff.fasta"/>
+      <output name="outfile2" file="file454.sff.qual"/>
+    -->
+    </test>
+  </tests>
+  <help>
+
+**If you use this tool, please cite:**
+
+| `Wagner G`_, Jardim R, Tschoeke DA, Loureiro DR, Ocana KACS, Ribeiro ACB, Emmel VE, 
+| Probst CM, Pitaluga AN, Grisard EC, Cavalcanti MC, Campos MLM, Mattoso M and `Dávila AMR`_
+| **STINGRAY: system for integrated genomic resources and analysis**
+| BMC Research Notes 2014, 7:132
+
+.. _Wagner G: glauber@ccb.ufsc.br
+.. _Dávila AMR: davila@ioc.fiocruz.br
+
+-----
+
+If you have any questions or comments, feel free to `contact  us`_. 
+
+.. _contact us: jardim@ioc.fiocruz.br
+
+-----
+
+**Sff_extract information**
+
+454 sequence reads are usually stored in sff files. In these files the information about the reads is stored: sequece, quality and quality and adapter clips. sff_extract extracts the reads from the sff files and stores them into fasta and xml or caf text files.
+sff_extract is a command line application written in python and it's free software distributed under the GPL licence. This software has been coded by Jose Blanca and Bastien Chevreux. See http://bioinf.comav.upv.es/sff_extract/index.html"
+  </help>
+
+</tool>
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