--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc/fastqc.xml	Tue Jun 07 17:22:05 2011 -0400
@@ -0,0 +1,94 @@
+<tool id="FastQC" name="FastQC" version="1.0.0">
+  <description>quality control checks on raw sequence data</description>
+  <command interpreter="python">fastqc.py
+   #if $input.extension.startswith( "fastq"):
+    --format=fastq
+   #else
+    --format=$input.extension
+   #end if
+   --input='$input'
+   --name='$input.name'
+   --dir='$report.extra_files_path'
+   --report='$report'
+   #if $contaminants != None and $contaminants != "None" and $contaminants != "":
+     --contaminants=$contaminants 
+   #end if
+  </command>
+  <inputs>
+   <param name="input" type="data" format="fastq,sam,bam" label="FASTQ reads" />
+   <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminants" 
+           help="Two fields per line separated by a TAB: name DNA_sequence.  For example: Illumina Small RNA RT Primer	CAAGCAGAAGACGGCATACGA"/>
+  </inputs>
+  <outputs>
+    <data name="report" format="html" />
+  </outputs>
+  <tests>
+    <!--
+    <test>
+      <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" />
+      <output name="output1_file" file="split_pair_reads_1.fastqsanger" />
+      <output name="output2_file" file="split_pair_reads_2.fastqsanger" />
+    </test>
+    -->
+  </tests>
+  <help>
+**What it does**
+
+FastQC_ is a product of Bioinformatics Group at the Babraham Institute.  FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
+
+The main functions of FastQC are::
+
+  - Import of data from BAM, SAM or FastQ files (any variant)
+  - Provding a quick overview to tell you in which areas there may be problems
+  - Summary graphs and tables to quickly assess your data
+  - Export of results to an HTML based permanent report
+  - Offline operation to allow automated generation of reports without running the interactive application
+
+
+.. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
+
+-----
+
+**Input format**
+
+Any fastq file, for example::
+
+    @HWI-EAS91_1_30788AAXX:7:21:1542:1758
+    GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
+    +HWI-EAS91_1_30788AAXX:7:21:1542:1758
+    hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
+
+**Contaminants format**
+
+An optional contaminant file (otherwise FastQC will use the default)::
+
+  # This file contains a list of potential contaminants which are
+  # frequently found in high throughput sequencing reactions.  These
+  # are mostly sequences of adapters / primers used in the various
+  # sequencing chemistries.
+  # 
+  # You can add more sequences to the file by putting one line per entry
+  # and specifying a name[tab]sequence.  If the contaminant you add is 
+  # likely to be of use to others please consider sending it to the FastQ
+  # authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/
+  # or by directly emailing simon.andrews@bbsrc.ac.uk so other users of
+  # the program can benefit.
+  Illumina Single End Apapter 1   ACACTCTTTCCCTACACGACGCTGTTCCATCT
+  Illumina Single End Apapter 2   CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+  Illumina Single End PCR Primer 1        AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+  Illumina Single End PCR Primer 2        CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+  Illumina Single End Sequencing Primer   ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+
+
+-----
+
+**Outputs**
+
+An HTML file with links to::
+
+  - fastqc_report.html
+  - summary.txt
+  - fastqc_data.txt
+
+  </help>
+</tool>