--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq-hts_1.0/galaxy/deseq.xml	Wed May 09 20:43:47 2012 -0400
@@ -0,0 +1,105 @@
+<tool id="deseq-hts" name="DESeq" version="1.6.0">
+  <description>Determines differentially expressed transcripts from read alignments</description>
+  <command> 
+deseq-hts/src/deseq-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat 
+#for $i in $replicate_groups
+#for $j in $i.replicates
+$j.bam_alignment:#slurp
+#end for
+#end for
+    >> $Log_File </command>
+  <inputs>
+	<param format="gff3" name="anno_input_selected" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/>
+   <repeat name="replicate_groups" title="Replicate group" min="2">
+     <repeat name="replicates" title="Replicate">
+      <param format="bam" name="bam_alignment" type="data" label="BAM alignment file" help="BAM alignment file. Can be generated from SAM files using the SAM Tools."/>
+     </repeat>
+   </repeat>
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="deseq_out" label="DESeq result"/>
+    <data format="txt" name="Log_File" label="DESeq log file"/>
+  </outputs>
+
+  <tests>
+    <test> 
+	command:
+	./deseq-hts.sh ../test_data/deseq_c_elegans_WS200-I-regions.gff3 ../test_data/deseq_c_elegans_WS200-I-regions_deseq.txt ../test_data/genes.mat ../test_data/deseq_c_elegans_WS200-I-regions-SRX001872.bam ../test_data/deseq_c_elegans_WS200-I-regions-SRX001875.bam
+	
+      <param name="anno_input_selected" value="deseq_c_elegans_WS200-I-regions.gff3" ftype="gff3" />
+      <param name="bam_alignments1" value="deseq_c_elegans_WS200-I-regions-SRX001872.bam" ftype="bam" />
+      <param name="bam_alignments2" value="deseq_c_elegans_WS200-I-regions-SRX001875.bam" ftype="bam" />
+      <output name="deseq_out" file="deseq_c_elegans_WS200-I-regions_deseq.txt" />
+    </test>
+  </tests> 
+
+  <help>
+
+.. class:: infomark
+
+**What it does** 
+
+`DESeq` is a tool for differential expression testing of RNA-Seq data.
+
+
+**Inputs**
+
+`DESeq` requires three input files to run:
+
+1. Annotation file in GFF3, containing the necessary information about the transcripts that are to be quantified.
+2. The BAM alignment files grouped into replicate groups, each containing several replicates. BAM files store the read alignments in a compressed format. They can be generated using the `SAM-to-BAM` tool in the NGS: SAM Tools section. (The script will also work with only two groups containing only a single replicate each. However, this analysis has less statistical power and is  therefor not recommended.)
+
+**Output**
+
+`DESeq` generates a text file containing the gene name and the p-value.
+
+------
+
+**Licenses**
+
+If **DESeq** is used to obtain results for scientific publications it
+should be cited as [1]_.
+
+**References** 
+
+.. [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`_. 
+
+.. _Differential expression analysis for sequence count data: http://dx.doi.org/10.1186/gb-2010-11-10-r106
+
+------
+
+.. class:: infomark
+
+**About formats**
+
+
+**GFF3 format** General Feature Format is a format for describing genes
+and other features associated with DNA, RNA and protein
+sequences. GFF3 lines have nine tab-separated fields:
+
+1. seqid - The name of a chromosome or scaffold.
+2. source - The program that generated this feature.
+3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". 
+4. start - The starting position of the feature in the sequence. The first base is numbered 1.
+5. stop - The ending position of the feature (inclusive).
+6. score - A score between 0 and 1000. If there is no score value, enter ".".
+7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
+8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
+9. attributes - All lines with the same group are linked together into a single item.
+
+For more information see http://www.sequenceontology.org/gff3.shtml
+
+**SAM/BAM format** The Sequence Alignment/Map (SAM) format is a
+tab-limited text format that stores large nucleotide sequence
+alignments. BAM is the binary version of a SAM file that allows for
+fast and intensive data processing. The format specification and the
+description of SAMtools can be found on
+http://samtools.sourceforge.net/.
+
+------
+
+DESeq-hts Wrapper Version 0.3 (Feb 2012)
+
+</help>
+</tool>