--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stringtie_merge.xml	Wed Jul 13 14:48:26 2016 -0400
@@ -0,0 +1,85 @@
+<tool id="stringtie_merge" name="StringTie" version="0.1.0">
+    <description>merge transcripts</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+    <![CDATA[
+        stringtie --merge
+        -p \${GALAXY_SLOTS:-1}
+        #if str($guide_gff) != "":
+            -G "$guide_gff"
+        #end if
+        -m $min_len
+        -c $min_cov
+        -F $min_fpkm
+        -T $min_tpm
+        -f $min_iso
+        -g $gap_len
+        $keep_introns
+        #set inputs = '" "'.join(str($input_gtf).split(','))
+        -o $out_gtf "$inputs"
+    ]]>
+    </command>
+    <inputs>
+        <param type="data" name="input_gtf" multiple="true" format="gtf,gff3" />
+        <param type="data" name="guide_gff" optional="True" format="gtf,gff3" />
+        <param argument="-m" type="integer" name="min_len" value="50" help="Minimum input transcript length to include in the merge" />
+        <param argument="-c" type="integer" name="min_cov" value="0" help="Minimum input transcript coverage to include in the merge" />
+        <param argument="-F" type="float" name="min_fpkm" value="1.0" help="Minimum input transcript FPKM to include in the merge" />
+        <param argument="-T" type="float" name="min_tpm" value="1.0" help="Minimum input transcript TPM to include in the merge" />
+        <param argument="-f" type="float" name="min_iso" value="0.01" help="Minimum isoform fraction" />
+        <param argument="-g" type="integer" name="gap_len" value="250" help="Gap between transcripts to merge together" />
+        <param argument="-i" type="boolean" truevalue="-i" falsevalue="" name="keep_introns" help="Keep merged transcripts with retained introns" />
+    </inputs>
+    <outputs>
+        <data name="out_gtf" format="gtf" />
+    </outputs>
+    <tests>
+        <test>
+            <param ftype="gtf" name="input_gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
+            <param ftype="gtf" name="guide_gff" value="stringtie_in.gtf" />
+            <output file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" name="out_gtf" />
+        </test>
+        <test>
+            <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
+            <param ftype="gtf" name="guide_gff" value="stringtie_merge_in3.gtf" />
+            <output file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" name="out_gtf" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does?**
+
+This is a special usage mode of StringTie_, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples. 
+
+If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts. 
+
+.. _StringTie: http://ccb.jhu.edu/software/stringtie/
+
+------
+
+StringTie --merge has the following options::
+
+  -G <guide_gff>   reference annotation to include in the merging (GTF/GFF3)
+  -o <out_gtf>     output file name for the merged transcripts GTF
+                    (default: stdout)
+  -m <min_len>     minimum input transcript length to include in the merge
+                    (default: 50)
+  -c <min_cov>     minimum input transcript coverage to include in the merge
+                    (default: 0)
+  -F <min_fpkm>    minimum input transcript FPKM to include in the merge
+                    (default: 1.0)
+  -T <min_tpm>     minimum input transcript TPM to include in the merge
+                    (default: 1.0)
+  -f <min_iso>     minimum isoform fraction (default: 0.01)
+  -g <gap_len>     gap between transcripts to merge together (default: 250)
+  -i               keep merged transcripts with retained introns; by default
+                   these are not kept unless there is strong evidence for them
+  -l <label>       name prefix for output transcripts (default: MSTRG)
+    ]]></help>
+    <expand macro="citations" />
+</tool>
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