--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer_build-icm.xml	Sat Jul 06 10:09:30 2013 -0400
@@ -0,0 +1,125 @@
+<tool id="glimmer_build-icm" name="Glimmer ICM builder" version="0.2">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="3.02b">glimmer</requirement>
+    </requirements>
+    <command>
+        build-icm
+            --depth $depth
+            #if $no_stops:
+                --no_stops
+            #end if
+            --period $period
+            --width $width
+
+            #if $stop_codon_opts.stop_codon_opts_selector == "gb":
+                --trans_table "${stop_codon_opts.genbank_gencode}"
+            #else:
+                --stop_codons "${stop_codon_opts.stop_codons}"
+            #end if
+
+            $outfile &lt; $infile 2>&#38;1;
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fasta" label="Trainings Dataset" help="A set of known genes in FASTA format." />
+        <param name="depth" type="integer" value="7" label="Set the depth of the ICM" help="The depth is the maximum number of positions in the context window that will be used to determine the probability of the predicted position." />
+        <param name="period" type="integer" value="3" label="Set the period of the ICM" help="The period is the number of different submodels for different positions in the text in a cyclic pattern. E.g., if the period is 3, the first submodel will determine positions 1, 4, 7, ..." />
+        <param name="width" type="integer" value="12" label="Set the width of the ICM" help="The width includes the predicted position." />
+        <param name="no_stops" type="boolean" truevalue="--no_stops" falsevalue="" checked="false" label="Do not use any input strings with in-frame stop codons" />
+
+        <conditional name="stop_codon_opts">
+            <param name="stop_codon_opts_selector" type="select" label="Specify start codons as">
+              <option value="gb" selected="True">Genbank translation table entry</option>
+              <option value="free_form">Comma-separated list</option>
+            </param>
+            <when value="gb">
+                <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons">
+                    <option value="1" select="True">1. Standard</option>
+                    <option value="2">2. Vertebrate Mitochondrial</option>
+                    <option value="3">3. Yeast Mitochondrial</option>
+                    <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
+                    <option value="5">5. Invertebrate Mitochondrial</option>
+                    <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
+                    <option value="9">9. Echinoderm Mitochondrial</option>
+                    <option value="10">10. Euplotid Nuclear</option>
+                    <option value="11">11. Bacteria and Archaea</option>
+                    <option value="12">12. Alternative Yeast Nuclear</option>
+                    <option value="13">13. Ascidian Mitochondrial</option>
+                    <option value="14">14. Flatworm Mitochondrial</option>
+                    <option value="15">15. Blepharisma Macronuclear</option>
+                    <option value="16">16. Chlorophycean Mitochondrial</option>
+                    <option value="21">21. Trematode Mitochondrial</option>
+                    <option value="22">22. Scenedesmus obliquus mitochondrial</option>
+                    <option value="23">23. Thraustochytrium Mitochondrial</option>
+                    <option value="24">24. Pterobranchia mitochondrial</option>
+                </param>
+            </when>
+            <when value="free_form">
+                <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="data" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value='streptomyces_Tu6071_plasmid_genes.fasta' />
+            <param name="depth" value="7" />
+            <param name="period" value="3" />
+            <param name="width" value="12" />
+            <param name="no_stops" value="" />
+            <param name="genbank_gencode" value="11" />
+            <!-- compare files sizes, because the output is a binary -->
+            <output name="outfile" file='streptomyces_Tu6071_plasmid_genes.icm' compare="sim_size" delta="1000" ftype="data" />
+        </test>
+    </tests>
+
+    <help>
+
+**What it does**
+
+This program constructs an interpolated context model (ICM) from an input set of sequences.
+
+This model can be used by Glimmer3 to predict genes.
+
+**TIP** To extract CDS from a GenBank file use the tool *Extract ORF from a GenBank file*.
+
+-----
+
+**Example**
+
+*Input*::
+
+	- Genome Sequence
+
+		>CELF22B7  C.aenorhabditis elegans (Bristol N2) cosmid F22B7
+		GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
+		GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
+		TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
+		TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
+		GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
+		ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
+		AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
+		CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
+		TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
+		AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
+		GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
+		AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
+		CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
+		AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
+		GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
+		.....
+
+*Output*::
+	interpolated context model (ICM)
+
+-------
+
+**References**
+
+A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).
+
+
+    </help>
+</tool>