--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tophat_fusion_post.xml	Mon Jan 27 13:16:59 2014 -0500
@@ -0,0 +1,53 @@
+<tool id="tophat_fusion_post" name="Tophat Fusion Post" version="0.1">
+    <description>post-processing to identify fusion genes</description>
+    <version_command>tophat-fusion-post --version</version_command>
+    <requirements>
+        <requirement type="package">tophat2</requirement>
+    </requirements>
+    <command>
+        ## Set up tophat_out structure.
+        mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out;
+
+        ## Set up blast directory structure.
+        #set blast_db_path = ${__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
+        ln -s ${blast_db_path}/ blast;
+
+        ## Set up additional files:
+	    ln -s ${blast_db_path}/refGene.txt .;
+	    ln -s ${blast_db_path}/ensGene.txt .;
+        ln -s ${blast_db_path}/mcl .;
+
+        ## Run tophat-fusion-post
+        tophat-fusion-post -p 22
+        --num-fusion-reads $num_fusion_reads --num-fusion-pairs $num_fusion_pairs --num-fusion-both $num_fusion_both --fusion-read-mismatches $fusion_read_mismatches --fusion-multireads $fusion_multireads
+        #if str($is_human) == 'No':
+              --non-human
+        #end if
+
+	## Bowtie2 indices.
+	${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
+    </command>
+
+    <inputs>
+        <param format="bam" name="accepted_hits" type="data" label="BAM file of aligned RNA-Seq reads" help=""/>
+        <param format="tabular" name="fusions" type="data" label="Tabular file of potential fusions" help=""/>
+        <param name="num_fusion_reads" type="integer" value="3" label="Num Fusion Reads" help="Fusions with at least this many supporting reads will be reported."/>
+        <param name="num_fusion_pairs" type="integer" value="2" label="Num Fusion Pairs" help="Fusions with at least this many supporting pairs will be reported."/>
+        <param name="num_fusion_both" type="integer" value="0" label="Num Fusion Reads + Pairs" help="The sum of supporting reads and pairs is at least this number for a fusion to be reported."/>
+        <param name="fusion_read_mismatches" type="integer" value="2" label="Fusion Read Mismatches" help="Reads support fusions if they map across fusion with at most this many mismatches."/>
+        <param name="fusion_multireads" type="integer" value="2" label="Reads that map to more than this many places will be ignored." help=""/>
+        <param name="is_human" type="select" label="Is your data from humans?">
+            <option value="Yes" selected="True">Yes</option>
+            <option value="No">No</option>
+        </param>
+    </inputs>
+
+    <stdio>
+        <regex match=".*" source="both" level="log" description="tool progress"/>
+    </stdio>
+
+    <outputs>
+        <data format="txt" name="results_txt" label="${tool.name} on ${on_string}: text results" from_work_dir="tophatfusion_out/result.txt"/>
+        <data format="html" name="results_html" label="${tool.name} on ${on_string}: html results" from_work_dir="tophatfusion_out/result.html"/>
+    </outputs>
+</tool>