--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/regtools_junctions_extract.xml	Wed Apr 12 17:44:58 2017 -0400
@@ -0,0 +1,138 @@
+<tool id="regtools_junctions_extract" name="regtools junctions extract" version="0.1.0">
+    <description>Extract splice junctions from a RNA-Seq BAM file</description>
+    <requirements>
+        <requirement type="package" version="0.3.0">regtools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        ## regtools expects an indexed BAM file
+        ## Use symlinks to link the BAM file and its index to the working directory
+        ## See: https://biostar.usegalaxy.org/p/10128/
+
+        ln -sf '${input1}' infile.bam &&
+        ln -sf '${input1.metadata.bam_index}' infile.bam.bai &&
+
+        regtools junctions extract
+          -i $min_intron_length
+          -I $max_intron_length
+          -o $output1
+          #if str($advanced_options.advanced_options_selector) == "on":
+            -a $advanced_options.min_anchor_length
+
+            #if str($advanced_options.region):
+                -r "$advanced_options.region"
+            #end if
+          #end if
+          infile.bam  &&
+        
+        python $__tool_directory__/validator.py $output1 $fixed_output
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="bam" />
+
+        <param name="min_intron_length" type="integer" label="Minimum intron length" value="20" min="1">
+            <help>Only considers spliced RNA-Seq reads with this minimum intron length (-i)</help>
+        </param>
+        <param name="max_intron_length" type="integer" label="Maximum intron length" value="500000" min="1">
+            <help>Only considers spliced RNA-Seq reads with this maximum intron length (-I)</help>
+        </param>
+
+        <conditional name="advanced_options">
+            <param name="advanced_options_selector" type="select" label="Advanced options">
+                <option value="off" selected="true">Hide advanced options</option>
+                <option value="on">Display advanced options</option>
+            </param>
+            <when value="on">
+                <param name="min_anchor_length" type="integer" label="Minimum anchor length" value="8" min="1">
+                    <help>Only report splice junctions with this minimum anchor length on both sides of the junction (-a)</help>
+                </param>
+                <param name="region" type="text" optional="true" label="Only extract junctions in this region" value="">
+                    <help>Only report splice junctions within this region (format = chrom:start-end) (-r)</help>
+                    <validator type="regex"
+                        message="Region should be in the following format: chrom:start-end">^([^:]+):(\d+)-(\d+)$</validator>
+                </param>
+            </when>
+
+            <when value="off" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output1" format="bed" label="${tool.name} on ${on_string}: original output"/>
+        <data name="fixed_output" format="bed" label="${tool.name} on ${on_string}: fixed_output for HAC workflow"/>
+    </outputs>
+    <tests>
+        <test>
+            <!-- Test with default parameters -->
+            <param name="input1" value="Dbia3_adult_males_shallow.bam" />
+            <output name="output1" file="Dbia3_adult_males_junctions_i20_I500000.bed" />
+            <output name="fixed_output" file="Dbia3_adult_males_junctions_i20_I500000_fixed.bed" />
+        </test>
+        <test>
+            <!-- Test with custom intron length thresholds -->
+            <param name="min_intron_length" value="50" />
+            <param name="max_intron_length" value="50000" />
+            <param name="input1" value="Dbia3_adult_males_shallow.bam" />
+            <output name="output1" file="Dbia3_adult_males_junctions_i50_I50000.bed" />
+            <output name="fixed_output" file="Dbia3_adult_males_junctions_i50_I50000_fixed.bed" />
+        </test>
+        <test>
+            <!-- Test with advanced option and custom anchor size -->
+            <param name="advanced_options_selector" value="on" />
+            <param name="min_anchor_length" value="10" />
+            <param name="input1" value="Dbia3_adult_males_shallow.bam" />
+            <output name="output1"
+                file="Dbia3_adult_males_junctions_i20_I500000_a10.bed" />
+            <output name="fixed_output"
+                file="Dbia3_adult_males_junctions_i20_I500000_a10_fixed.bed" />
+        </test>
+        <test>
+            <!-- Test with advanced option and selected region -->
+            <param name="advanced_options_selector" value="on" />
+            <param name="region" value="contig2:10000-30000" />
+            <param name="input1" value="Dbia3_adult_males_shallow.bam" />
+            <output name="output1" file="Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb.bed" />
+            <output name="fixed_output" file="Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb_fixed.bed"/>
+        </test>
+        <test>
+            <!--Test with output having invalid strand -->
+            <param name="input1" value="Dbia3.bam" />
+            <output name="output1" file="Dbia3_i20_I500000.bed" />
+            <output name="fixed_output" file="Dbia3_i20_I500000_fixed.bed" />  
+        </test>   
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+The `regtools junctions extract <https://regtools.readthedocs.io/en/latest/commands/junctions-extract/>`_
+tool creates a list of exon-exon junctions from spliced RNA-Seq reads within a BAM
+alignment file. The format of the output BED file is similar to the ``junctions.bed``
+file produced by TopHat2.
+
+The extent of each BED feature corresponds to the maximum overhang of each splice
+junction. The score of each BED feature corresponds to the number of spliced RNA-Seq
+reads that support each junction.
+
+--------
+
+.. class:: warningmark
+
+By default, the minimum intron size is **20 bp** and the maximum intron size is
+**500,000 bp** so that they conform to the default intron size settings for
+`HISAT2 <https://ccb.jhu.edu/software/hisat2/manual.shtml#options>`_. The minimum
+intron size for the command-line version of ``regtools junctions extract`` is 70 bp.
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubregtools,
+  author = {Griffith Lab},
+  year = {2016},
+  title = {regtools},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/griffithlab/regtools},
+}</citation>
+    </citations>
+</tool>