# HG changeset patch
# User iuc
# Date 1491325107 14400
# Node ID c84d44519b2eb12254957ce64ea04832edff3d72
# Parent  1f23fc7df25c066d999a2a2d666afbd020c79318
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103

diff -r 1f23fc7df25c -r c84d44519b2e macros.xml
--- a/macros.xml	Tue Mar 21 03:07:22 2017 -0400
+++ b/macros.xml	Tue Apr 04 12:58:27 2017 -0400
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-        <requirement type="package" version="1.2.3">stringtie</requirement>
+        <requirement type="package" version="1.3.3">stringtie</requirement>
             <yield/>
         </requirements>
     </xml>
diff -r 1f23fc7df25c -r c84d44519b2e stringtie.xml
--- a/stringtie.xml	Tue Mar 21 03:07:22 2017 -0400
+++ b/stringtie.xml	Tue Apr 04 12:58:27 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="stringtie" name="StringTie" version="1.2.3">
+<tool id="stringtie" name="StringTie" version="1.3.3">
     <description>transcript assembly and quantification</description>
     <macros>
         <import>macros.xml</import>
@@ -8,28 +8,36 @@
     <expand macro="version_command" />
     <command>
     <![CDATA[
+        mkdir -p ./special_de_output/sample1/ &&
+        #if str($guide.use_guide) == 'yes':
+            ln -s '$guide.guide_gff' ./special_de_output/sample1/guide.gtf &&
+        #end if
+
         #if $input_bam.metadata.ftype == 'sam':
-            samtools sort -@ \${GALAXY_SLOTS:-1} "$input_bam" | stringtie
+            samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' | stringtie
         #else
-            stringtie "$input_bam"
+            stringtie '$input_bam'
         #end if
+
         -o "$output_gtf"
         -p "\${GALAXY_SLOTS:-1}"
         #if str($guide.use_guide) == 'yes':
-            -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
-            #if $guide.output_ballgown:
-                -b .
+            -C '$coverage'
+            -G '$guide.guide_gff'
+            $guide.input_estimation
+            #if $guide.special_outputs != 'no':
+                -b ./special_de_output/sample1/
             #end if
         #end if
         #if str($option_set.options) == 'advanced':
-            -l "$option_set.name_prefix"
-            -f "$option_set.fraction"
-            -m "$option_set.min_tlen"
-            -a "$option_set.min_anchor_len"
-            -j "$option_set.min_anchor_cov"
-            -c "$option_set.min_bundle_cov"
-            -g "$option_set.bdist"
-            -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
+            -l '$option_set.name_prefix'
+            -f '$option_set.fraction'
+            -m '$option_set.min_tlen'
+            -a '$option_set.min_anchor_len'
+            -j '$option_set.min_anchor_cov'
+            -c '$option_set.min_bundle_cov'
+            -g '$option_set.bdist'
+            -M '$option_set.bundle_fraction' $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
             #if $option_set.abundance_estimation:
                 -A "$gene_abundance_estimation"
             #end if
@@ -37,20 +45,63 @@
                 -x "$option_set.omit_sequences"
             #end if
         #end if
+
+        #if str($guide.use_guide) == 'yes':
+            #if $guide.special_outputs.special_outputs_select == 'deseq2':
+                &&
+                prepDE.py
+                    -i ./special_de_output/
+                    -g gene_cout_matrix.tsv
+                    -t transcripts_count_matrix.tsv
+                    -l $guide.special_outputs.read_length
+                    #if str($option_set.options) == 'advanced':
+                        -s '$option_set.name_prefix'
+                    #end if
+                    #if $guide.special_outputs.clustering:
+                        -c
+                        --legend ./legend.tsv
+
+                        &&
+                        sed -i.bak 's/,/\t/g' ./legend.tsv
+
+                    #end if
+                &&
+                sed -i.bak 's/,/\t/g' transcripts_count_matrix.tsv
+                &&
+                sed -i.bak 's/,/\t/g' gene_cout_matrix.tsv
+            #end if
+        #end if
+
     ]]>
     </command>
     <inputs>
         <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
         <conditional name="guide">
             <param label="Use GFF file to guide assembly" name="use_guide" type="select">
-                <option value="yes">Use GFF</option>
-                <option selected="True" value="no">Do not use GFF</option>
+                <option value="yes">Use GFF/GTF</option>
+                <option selected="True" value="no">Do not use GFF/GTF</option>
             </param>
             <when value="no" />
             <when value="yes">
-                <param argument="-G" format="gtf,gff3" help="" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
-                <param argument="-e" falsevalue="" help="" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />
-                <param argument="-b" falsevalue="" help="" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />
+                <param argument="-G" format="gtf,gff3" name="guide_gff" type="data" 
+                       help="" label="Reference annotation to use for guiding the assembly process" />
+                <param argument="-e" name="input_estimation" truevalue="-e" type="boolean" falsevalue=""
+                       help="" label="Perform abundance estimation only of input transcripts" />
+                <conditional name="special_outputs">
+                    <param label="Output additional files for use in..." name="special_outputs_select" type="select">
+                        <option value="ballgown">Ballgown</option>
+                        <option selected="True" value="deseq2">DESeq2/EdgeR</option>
+                        <option value="no">No addional output</option>
+                    </param>
+                    <when value="ballgown" />
+                    <when value="deseq2">
+                        <param label="Average read length" name="read_length" type="integer" value="75" help="" />
+                        <param label="Whether to cluster genes that overlap with different gene IDs"
+                               name="clustering"
+                               truevalue="--cluster"
+                               type="boolean" help="ignoring ones with geneID pattern" falsevalue="" />
+                    </when>
+                </conditional>
             </when>
         </conditional>
         <conditional name="option_set">
@@ -60,19 +111,24 @@
             </param>
             <when value="default" />
             <when value="advanced">
-                <param argument="-t" falsevalue="" help="" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
-                <param argument="-S" falsevalue="" help="" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
-                <param argument="-l" help="" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
-                <param argument="-f" help="" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
-                <param argument="-m" help="" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
-                <param argument="-a" help="" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
-                <param argument="-j" help="" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
-                <param argument="-c" help="" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
-                <param argument="-g" help="" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
-                <param argument="-M" help="" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
-                <param argument="-x" help="e.g. chrM,chrX" label="Do not assemble any transcripts on these reference sequence(s)" name="omit_sequences" type="text" value="" />
-                <param argument="-A" falsevalue="" help="" label="Additional gene abundance estimation output file" name="abundance_estimation" truevalue="-A" type="boolean" />
-                <param argument="-u" falsevalue="" help="" label="Disable multi-mapping correction" name="multi_mapping" truevalue="-u" type="boolean" />
+                <param argument="-t" falsevalue="" name="disable_trimming" truevalue="-t" type="boolean"
+                    label="Disable trimming of predicted transcripts based on coverage" />
+                <param argument="-S" falsevalue="" 
+                    label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
+                <param argument="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
+                <param argument="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
+                <param argument="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
+                <param argument="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
+                <param argument="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
+                <param argument="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
+                <param argument="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
+                <param argument="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
+                <param argument="-x" name="omit_sequences" type="text" value="" 
+                    help="e.g. chrM,chrX" label="Do not assemble any transcripts on these reference sequence(s)" />
+                <param argument="-A" falsevalue="" name="abundance_estimation" truevalue="-A" type="boolean"
+                    label="Additional gene abundance estimation output file" />
+                <param argument="-u" falsevalue="" truevalue="-u" type="boolean"
+                    label="Disable multi-mapping correction" name="multi_mapping" />
             </when>
         </conditional>
     </inputs>
@@ -84,20 +140,38 @@
         <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
             <filter>guide['use_guide'] == 'yes'</filter>
         </data>
-        <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
-            <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
+        <data format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
+            label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
+            <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
+        </data>
+        <data format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
+            label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
+            <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
         </data>
-        <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
-            <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
+        <data format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
+            label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
+            <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
+        </data>
+        <data format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
+            label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
+            <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
         </data>
-        <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
-            <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
+        <data format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
+            label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
+            <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
         </data>
-        <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
-            <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
+        
+        <data format="tabular" from_work_dir="gene_cout_matrix.tsv"
+            label="${tool.name} on ${on_string}: Gene counts" name="gene_counts">
+            <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
         </data>
-        <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
-            <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
+        <data format="tabular" from_work_dir="transcripts_count_matrix.tsv"
+            label="${tool.name} on ${on_string}: Transcript counts" name="transcript_counts">
+            <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
+        </data>
+        <data format="tabular" from_work_dir="legend.tsv"
+            label="${tool.name} on ${on_string}: legend" name="legend">
+            <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' and guide['special_outputs']['clustering'] is True</filter>
         </data>
     </outputs>
     <tests>
@@ -117,6 +191,7 @@
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="yes" />
+            <param name="special_outputs_select" value="no" />
             <param name="guide_gff" value="stringtie_in.gtf" />
             <param name="options" value="default" />
             <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
@@ -124,6 +199,7 @@
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="yes" />
+            <param name="special_outputs_select" value="no" />
             <param name="guide_gff" value="stringtie_in.gtf" />
             <param name="options" value="advanced" />
             <param name="fraction" value="0.17" />
@@ -132,35 +208,50 @@
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="yes" />
-            <param name="output_ballgown" value="yes" />
+            <param name="special_outputs_select" value="ballgown" />
             <param name="guide_gff" value="stringtie_in.gtf" />
             <param name="options" value="default" />
-            <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
-            <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
-            <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
-            <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
-            <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
+            <output file="./ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
+            <output file="./ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
+            <output file="./ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
+            <output file="./ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
+            <output file="./ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
             <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
             <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
         </test>
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="yes" />
+            <param name="special_outputs_select" value="deseq2" />
+            <param name="input_estimation" value="True" />
+            <param name="guide_gff" value="stringtie_in.gtf" />
+            <param name="options" value="default" />
+            <param name="clustering" value="True" />
+            <output file="./deseq2/gene_counts.tsv" ftype="tabular" lines_diff="2" name="gene_counts" />
+            <output file="./deseq2/transcript_counts.tsv" ftype="tabular" name="transcript_counts" />
+            <output file="./deseq2/legend.tsv" ftype="tabular" name="legend" />
+            <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
+            <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
+        </test>
+        <test>
+            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
+            <param name="use_guide" value="yes" />
             <param name="guide_gff" value="stringtie_in.gtf" />
             <param name="options" value="advanced" />
             <param name="fraction" value="0.17" />
             <param name="abundance_estimation" value="True" />
             <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
-            <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" />
+            <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" />
         </test>
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="yes" />
+            <param name="special_outputs_select" value="no" />
             <param name="guide_gff" value="stringtie_in.gtf" />
             <param name="options" value="advanced" />
             <param name="fraction" value="0.15" />
             <param name="c" value="test_chromosome" />
-            <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
+            <output file="stringtie_out8.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
         </test>
     </tests>
     <help>
diff -r 1f23fc7df25c -r c84d44519b2e stringtie_merge.xml
--- a/stringtie_merge.xml	Tue Mar 21 03:07:22 2017 -0400
+++ b/stringtie_merge.xml	Tue Apr 04 12:58:27 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="stringtie_merge" name="StringTie" version="0.1.0">
+<tool id="stringtie_merge" name="StringTie" version="1.3.3">
     <description>merge transcripts</description>
     <macros>
         <import>macros.xml</import>
diff -r 1f23fc7df25c -r c84d44519b2e test-data/ballgown/t_data.ctab
--- a/test-data/ballgown/t_data.ctab	Tue Mar 21 03:07:22 2017 -0400
+++ b/test-data/ballgown/t_data.ctab	Tue Apr 04 12:58:27 2017 -0400
@@ -1,2 +1,2 @@
 t_id	chr	strand	start	end	t_name	num_exons	length	gene_id	gene_name	cov	FPKM
-1	test_chromosome	+	53	550	CUFF.1.1	3	298	CUFF.1	.	44.724823	3276543.750000
+1	test_chromosome	+	53	550	CUFF.1.1	3	298	CUFF.1	.	44.070122	3228580.250000
diff -r 1f23fc7df25c -r c84d44519b2e test-data/deseq2/gene_counts.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/deseq2/gene_counts.tsv	Tue Apr 04 12:58:27 2017 -0400
@@ -0,0 +1,2 @@
+	sample1
+CUFF.1	574
diff -r 1f23fc7df25c -r c84d44519b2e test-data/deseq2/legend.tsv
diff -r 1f23fc7df25c -r c84d44519b2e test-data/deseq2/transcript_counts.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/deseq2/transcript_counts.tsv	Tue Apr 04 12:58:27 2017 -0400
@@ -0,0 +1,2 @@
+	sample1
+CUFF.1.1	574
diff -r 1f23fc7df25c -r c84d44519b2e test-data/e2t.ctab
diff -r 1f23fc7df25c -r c84d44519b2e test-data/e_data.ctab
diff -r 1f23fc7df25c -r c84d44519b2e test-data/i2t.ctab
diff -r 1f23fc7df25c -r c84d44519b2e test-data/i_data.ctab
diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_merge_out1.gtf
--- a/test-data/stringtie_merge_out1.gtf	Tue Mar 21 03:07:22 2017 -0400
+++ b/test-data/stringtie_merge_out1.gtf	Tue Apr 04 12:58:27 2017 -0400
@@ -1,5 +1,5 @@
-# stringtie --merge -p 1 -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_5.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_6.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_1.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_2.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_3.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_4.dat
-# StringTie version 1.2.3
+# stringtie --merge -p 1 -G /tmp/tmpJfKWNy/files/000/dataset_42.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpJfKWNy/files/000/dataset_43.dat /tmp/tmpJfKWNy/files/000/dataset_38.dat /tmp/tmpJfKWNy/files/000/dataset_39.dat /tmp/tmpJfKWNy/files/000/dataset_40.dat /tmp/tmpJfKWNy/files/000/dataset_41.dat
+# StringTie version 1.3.3
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; ref_gene_id "CUFF.1"; 
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "1"; ref_gene_id "CUFF.1"; 
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "2"; ref_gene_id "CUFF.1"; 
diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_merge_out2.gtf
--- a/test-data/stringtie_merge_out2.gtf	Tue Mar 21 03:07:22 2017 -0400
+++ b/test-data/stringtie_merge_out2.gtf	Tue Apr 04 12:58:27 2017 -0400
@@ -1,5 +1,5 @@
-# stringtie --merge -p 1 -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_9.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_10.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_7.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_8.dat
-# StringTie version 1.2.3
+# stringtie --merge -p 1 -G /tmp/tmpJfKWNy/files/000/dataset_46.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpJfKWNy/files/000/dataset_47.dat /tmp/tmpJfKWNy/files/000/dataset_44.dat /tmp/tmpJfKWNy/files/000/dataset_45.dat
+# StringTie version 1.3.3
 chr1	StringTie	transcript	3189811	3193042	1000	.	.	gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; 
 chr1	StringTie	exon	3189811	3193042	1000	.	.	gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; 
 chr1	StringTie	transcript	3200023	3200191	1000	.	.	gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; 
@@ -47,54 +47,54 @@
 chr1	StringTie	transcript	3450907	3451109	1000	.	.	gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; 
 chr1	StringTie	exon	3450907	3451109	1000	.	.	gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; exon_number "1"; 
 chr1	mm9_refFlat	transcript	4334224	4350473	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1";
-chr1	mm9_refFlat	exon	4334224	4340172	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "1"; ref_gene_id "Rp1";
-chr1	mm9_refFlat	exon	4341991	4342162	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "2"; ref_gene_id "Rp1";
-chr1	mm9_refFlat	exon	4342283	4342918	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "3"; ref_gene_id "Rp1";
-chr1	mm9_refFlat	exon	4350281	4350473	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "4"; ref_gene_id "Rp1";
+chr1	mm9_refFlat	exon	4334224	4340172	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "1";
+chr1	mm9_refFlat	exon	4341991	4342162	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "2";
+chr1	mm9_refFlat	exon	4342283	4342918	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "3";
+chr1	mm9_refFlat	exon	4350281	4350473	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "4";
 chr1	mm9_refFlat	transcript	4481009	4486494	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17";
-chr1	mm9_refFlat	exon	4481009	4482749	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "1"; ref_gene_id "Sox17";
-chr1	mm9_refFlat	exon	4483181	4483547	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "2"; ref_gene_id "Sox17";
-chr1	mm9_refFlat	exon	4483853	4483944	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "3"; ref_gene_id "Sox17";
-chr1	mm9_refFlat	exon	4485217	4486023	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "4"; ref_gene_id "Sox17";
-chr1	mm9_refFlat	exon	4486372	4486494	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "5"; ref_gene_id "Sox17";
+chr1	mm9_refFlat	exon	4481009	4482749	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "1";
+chr1	mm9_refFlat	exon	4483181	4483547	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "2";
+chr1	mm9_refFlat	exon	4483853	4483944	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "3";
+chr1	mm9_refFlat	exon	4485217	4486023	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "4";
+chr1	mm9_refFlat	exon	4486372	4486494	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "5";
 chr1	mm9_refFlat	transcript	4763279	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4763279	4766882	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4774032	4774186	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5"; ref_gene_id "Mrpl15";
+chr1	mm9_refFlat	exon	4763279	4766882	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1";
+chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2";
+chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3";
+chr1	mm9_refFlat	exon	4774032	4774186	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4";
+chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5";
 chr1	mm9_refFlat	transcript	4763279	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4763279	4764597	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "1"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4774032	4774186	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5"; ref_gene_id "Mrpl15";
+chr1	mm9_refFlat	exon	4763279	4764597	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "1";
+chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2";
+chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3";
+chr1	mm9_refFlat	exon	4774032	4774186	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4";
+chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5";
 chr1	mm9_refFlat	transcript	4763279	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4763279	4764597	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "1"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4"; ref_gene_id "Mrpl15";
+chr1	mm9_refFlat	exon	4763279	4764597	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "1";
+chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2";
+chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3";
+chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4";
 chr1	mm9_refFlat	transcript	4797974	4836816	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1";
-chr1	mm9_refFlat	exon	4797974	4798063	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1"; ref_gene_id "Lypla1";
-chr1	mm9_refFlat	exon	4798536	4798567	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2"; ref_gene_id "Lypla1";
-chr1	mm9_refFlat	exon	4818665	4818730	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3"; ref_gene_id "Lypla1";
-chr1	mm9_refFlat	exon	4820349	4820396	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4"; ref_gene_id "Lypla1";
-chr1	mm9_refFlat	exon	4822392	4822462	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5"; ref_gene_id "Lypla1";
-chr1	mm9_refFlat	exon	4827082	4827155	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6"; ref_gene_id "Lypla1";
-chr1	mm9_refFlat	exon	4829468	4829569	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7"; ref_gene_id "Lypla1";
-chr1	mm9_refFlat	exon	4831037	4831213	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8"; ref_gene_id "Lypla1";
-chr1	mm9_refFlat	exon	4835044	4836816	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9"; ref_gene_id "Lypla1";
+chr1	mm9_refFlat	exon	4797974	4798063	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1";
+chr1	mm9_refFlat	exon	4798536	4798567	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2";
+chr1	mm9_refFlat	exon	4818665	4818730	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3";
+chr1	mm9_refFlat	exon	4820349	4820396	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4";
+chr1	mm9_refFlat	exon	4822392	4822462	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5";
+chr1	mm9_refFlat	exon	4827082	4827155	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6";
+chr1	mm9_refFlat	exon	4829468	4829569	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7";
+chr1	mm9_refFlat	exon	4831037	4831213	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8";
+chr1	mm9_refFlat	exon	4835044	4836816	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9";
 chr1	mm9_refFlat	transcript	4847775	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4847775	4848057	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4857551	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2"; ref_gene_id "Tcea1";
+chr1	mm9_refFlat	exon	4847775	4848057	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1";
+chr1	mm9_refFlat	exon	4857551	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2";
 chr1	mm9_refFlat	transcript	4847775	4887987	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4847775	4848057	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4857551	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4868108	4868213	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4876825	4876912	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4879538	4879683	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4880821	4880877	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4881996	4882150	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4883498	4883644	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4885015	4885086	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4886437	4887987	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10"; ref_gene_id "Tcea1";
+chr1	mm9_refFlat	exon	4847775	4848057	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1";
+chr1	mm9_refFlat	exon	4857551	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2";
+chr1	mm9_refFlat	exon	4868108	4868213	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3";
+chr1	mm9_refFlat	exon	4876825	4876912	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4";
+chr1	mm9_refFlat	exon	4879538	4879683	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5";
+chr1	mm9_refFlat	exon	4880821	4880877	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6";
+chr1	mm9_refFlat	exon	4881996	4882150	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7";
+chr1	mm9_refFlat	exon	4883498	4883644	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8";
+chr1	mm9_refFlat	exon	4885015	4885086	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9";
+chr1	mm9_refFlat	exon	4886437	4887987	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10";
diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out1.gtf
--- a/test-data/stringtie_out1.gtf	Tue Mar 21 03:07:22 2017 -0400
+++ b/test-data/stringtie_out1.gtf	Tue Apr 04 12:58:27 2017 -0400
@@ -1,6 +1,6 @@
-# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_1.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_2.dat -p 1
-# StringTie version 1.2.3
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "975770.250000";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.948147";
+# stringtie /tmp/tmpJfKWNy/files/000/dataset_1.dat -o /tmp/tmpJfKWNy/files/000/dataset_2.dat -p 1
+# StringTie version 1.3.3
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.060520"; FPKM "3227877.000000"; TPM "962189.250000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.012157";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565";
 test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000";
diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out2.gtf
--- a/test-data/stringtie_out2.gtf	Tue Mar 21 03:07:22 2017 -0400
+++ b/test-data/stringtie_out2.gtf	Tue Apr 04 12:58:27 2017 -0400
@@ -1,6 +1,6 @@
-# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_9.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_10.dat -p 1 -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 1.2.3
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "975770.250000";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.948147";
+# stringtie /tmp/tmpJfKWNy/files/000/dataset_3.dat -o /tmp/tmpJfKWNy/files/000/dataset_4.dat -p 1 -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
+# StringTie version 1.3.3
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.060520"; FPKM "3227877.000000"; TPM "962189.250000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.012157";
 test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565";
 test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000";
diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out3.gtf
--- a/test-data/stringtie_out3.gtf	Tue Mar 21 03:07:22 2017 -0400
+++ b/test-data/stringtie_out3.gtf	Tue Apr 04 12:58:27 2017 -0400
@@ -1,6 +1,6 @@
-# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_16.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_18.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_20.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_17.dat
-# StringTie version 1.2.3
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000";
+# stringtie /tmp/tmpJfKWNy/files/000/dataset_5.dat -o /tmp/tmpJfKWNy/files/000/dataset_7.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_8.dat -G /tmp/tmpJfKWNy/files/000/dataset_6.dat -b ./special_de_output/sample1/
+# StringTie version 1.3.3
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.070122"; FPKM "3228580.250000"; TPM "962398.937500";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "48.005386";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.452003";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.104616";
diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out4.gtf
--- a/test-data/stringtie_out4.gtf	Tue Mar 21 03:07:22 2017 -0400
+++ b/test-data/stringtie_out4.gtf	Tue Apr 04 12:58:27 2017 -0400
@@ -1,6 +1,6 @@
-# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_1.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_3.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_5.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_2.dat -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_4.dat
-# StringTie version 1.2.3
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000";
+# stringtie /tmp/tmpJfKWNy/files/000/dataset_28.dat -o /tmp/tmpJfKWNy/files/000/dataset_30.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_32.dat -G /tmp/tmpJfKWNy/files/000/dataset_29.dat -b ./special_de_output/sample1/ -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /tmp/tmpJfKWNy/files/000/dataset_31.dat
+# StringTie version 1.3.3
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.070122"; FPKM "3228580.250000"; TPM "962398.937500";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "48.005386";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.452003";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.104616";
diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out5.gtf
--- a/test-data/stringtie_out5.gtf	Tue Mar 21 03:07:22 2017 -0400
+++ b/test-data/stringtie_out5.gtf	Tue Apr 04 12:58:27 2017 -0400
@@ -1,6 +1,6 @@
-# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_25.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_27.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_29.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_26.dat -B
-# StringTie version 1.2.3
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000";
+# stringtie /tmp/tmpJfKWNy/files/000/dataset_13.dat -o /tmp/tmpJfKWNy/files/000/dataset_15.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_16.dat -G /tmp/tmpJfKWNy/files/000/dataset_14.dat -b ./special_de_output/sample1/
+# StringTie version 1.3.3
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.070122"; FPKM "3228580.250000"; TPM "962398.937500";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "48.005386";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.452003";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.104616";
diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out6.gtf
--- a/test-data/stringtie_out6.gtf	Tue Mar 21 03:07:22 2017 -0400
+++ b/test-data/stringtie_out6.gtf	Tue Apr 04 12:58:27 2017 -0400
@@ -1,3 +1,6 @@
-Gene ID	Gene Name	Reference	Strand	Start	End	Coverage	FPKM	TPM
-CUFF.1	-	test_chromosome	+	53	550	45.791946	3354721.250000	1000000.062500
-STRG.1	-	test_chromosome	+	53	550	45.791946	3354721.250000	1000000.062500
+# stringtie /tmp/tmpJfKWNy/files/000/dataset_22.dat -o /tmp/tmpJfKWNy/files/000/dataset_24.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_25.dat -G /tmp/tmpJfKWNy/files/000/dataset_23.dat -e -b ./special_de_output/sample1/
+# StringTie version 1.3.3
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; cov "45.795296"; FPKM "3354966.750000"; TPM "1000000.000000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; cov "49.777779";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; cov "54.160004";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; cov "21.660000";
diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out7.gtf
--- a/test-data/stringtie_out7.gtf	Tue Mar 21 03:07:22 2017 -0400
+++ b/test-data/stringtie_out7.gtf	Tue Apr 04 12:58:27 2017 -0400
@@ -1,6 +1,3 @@
-# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_39.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_41.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_42.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_40.dat -l STRG -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 1.2.3
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000";
+Gene ID	Gene Name	Reference	Strand	Start	End	Coverage	FPKM	TPM
+CUFF.1	-	test_chromosome	+	53	550	45.791946	3354721.250000	1000000.062500
+STRG.1	-	test_chromosome	+	53	550	45.791946	3354721.250000	1000000.062500
diff -r 1f23fc7df25c -r c84d44519b2e test-data/stringtie_out8.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out8.gtf	Tue Apr 04 12:58:27 2017 -0400
@@ -0,0 +1,6 @@
+# stringtie /tmp/tmpJfKWNy/files/000/dataset_34.dat -o /tmp/tmpJfKWNy/files/000/dataset_36.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_37.dat -G /tmp/tmpJfKWNy/files/000/dataset_35.dat -b ./special_de_output/sample1/ -l STRG -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
+# StringTie version 1.3.3
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.070122"; FPKM "3228580.250000"; TPM "962398.937500";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "48.005386";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.452003";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.104616";
diff -r 1f23fc7df25c -r c84d44519b2e test-data/t_data.ctab
diff -r 1f23fc7df25c -r c84d44519b2e tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Mar 21 03:07:22 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="stringtie" version="1.2.3">
-      <repository changeset_revision="ee804c6f3b97" name="package_stringtie_1_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>