# HG changeset patch
# User iuc
# Date 1431658060 14400
# Node ID 6884408acc4468775e68425c27c951e482e3d114
# Parent  d06ccb1812fffb95d77b89d53d2991515e7544a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389

diff -r d06ccb1812ff -r 6884408acc44 stringtie.xml
--- a/stringtie.xml	Wed Apr 29 12:07:07 2015 -0400
+++ b/stringtie.xml	Thu May 14 22:47:40 2015 -0400
@@ -1,7 +1,7 @@
-<tool id="stringtie" name="StringTie" version="1.0.1">
-    <description>RNA-Seq assembler</description>
+<tool id="stringtie" name="StringTie" version="1.0.3">
+    <description>transcript assembly and quantification</description>
     <requirements>
-        <requirement type="package" version="1.0.1">stringtie</requirement>
+        <requirement type="package" version="1.0.3">stringtie</requirement>
     </requirements>
     <command><![CDATA[
 stringtie "$input_bam"
@@ -27,7 +27,7 @@
 ]]>
 </command>
     <inputs>
-        <param format="bam" label="BAM file to assemble" name="input_bam" type="data" />
+        <param format="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>
@@ -35,9 +35,9 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <param format="gtf,gff3" help="(-G)" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
-                <param falsevalue="" help="(-e)" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />
-                <param falsevalue="" help="(-b)" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />
+                <param format="gtf,gff3" help="-G" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
+                <param falsevalue="" help="-e" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />
+                <param falsevalue="" help="-b" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />
             </when>
         </conditional>
         <conditional name="option_set">
@@ -47,17 +47,17 @@
             </param>
             <when value="default" />
             <when value="advanced">
-                <param falsevalue="" help="(-t)" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
-                <param falsevalue="" help="(-S)" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
-                <param help="(-l)" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
-                <param help="(-f)" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
-                <param help="(-m)" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
-                <param help="(-a)" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
-                <param help="(-j)" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
-                <param help="(-c)" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
-                <param help="(-s)" label="Coverage saturation threshold" name="maxcov" type="integer" value="1000000" />
-                <param help="(-g)" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
-                <param help="(-M)" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
+                <param falsevalue="" help="-t" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
+                <param falsevalue="" help="-S" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
+                <param help="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
+                <param help="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
+                <param help="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
+                <param help="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
+                <param help="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
+                <param help="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
+                <param help="-s" label="Coverage saturation threshold" name="maxcov" type="integer" value="1000000" />
+                <param help="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
+                <param help="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
             </when>
         </conditional>
     </inputs>
@@ -128,15 +128,17 @@
     </tests>
     <help>
 <![CDATA[
-StringTie v1.0.1 usage:
- stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
-  [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens]
-  [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>]
-  {-B | -b <dir_path>} [-e]
+
+**What it does?**
+
+StringTie_ is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional *de novo* assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.
 
-Assemble RNA-Seq alignments into potential transcripts.
- 
- Options:
+.. _StringTie: http://ccb.jhu.edu/software/stringtie/
+
+------
+
+StringTie has the following options::
+
  -G reference annotation to use for guiding the assembly process (GTF/GFF3)
  -l name prefix for output transcripts (default: STRG)
  -f minimum isoform fraction (default: 0.1)
diff -r d06ccb1812ff -r 6884408acc44 test-data/stringtie_out1.gtf
--- a/test-data/stringtie_out1.gtf	Wed Apr 29 12:07:07 2015 -0400
+++ b/test-data/stringtie_out1.gtf	Thu May 14 22:47:40 2015 -0400
@@ -1,4 +1,4 @@
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.724823";FPKM "3276543.750000";
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.724823"; FPKM "3276543.750000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.011967";
 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 d06ccb1812ff -r 6884408acc44 test-data/stringtie_out2.gtf
--- a/test-data/stringtie_out2.gtf	Wed Apr 29 12:07:07 2015 -0400
+++ b/test-data/stringtie_out2.gtf	Thu May 14 22:47:40 2015 -0400
@@ -1,4 +1,4 @@
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.724823";FPKM "3276543.750000";
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.724823"; FPKM "3276543.750000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.011967";
 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 d06ccb1812ff -r 6884408acc44 test-data/stringtie_out3.gtf
--- a/test-data/stringtie_out3.gtf	Wed Apr 29 12:07:07 2015 -0400
+++ b/test-data/stringtie_out3.gtf	Thu May 14 22:47:40 2015 -0400
@@ -1,4 +1,4 @@
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; 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"; 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"; cov "21.090000";
+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";
+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";
diff -r d06ccb1812ff -r 6884408acc44 test-data/stringtie_out4.gtf
--- a/test-data/stringtie_out4.gtf	Wed Apr 29 12:07:07 2015 -0400
+++ b/test-data/stringtie_out4.gtf	Thu May 14 22:47:40 2015 -0400
@@ -1,4 +1,4 @@
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; 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"; 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"; cov "21.090000";
+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";
+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";
diff -r d06ccb1812ff -r 6884408acc44 test-data/stringtie_out5.gtf
--- a/test-data/stringtie_out5.gtf	Wed Apr 29 12:07:07 2015 -0400
+++ b/test-data/stringtie_out5.gtf	Thu May 14 22:47:40 2015 -0400
@@ -1,4 +1,4 @@
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; 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"; 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"; cov "21.090000";
+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";
+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";
diff -r d06ccb1812ff -r 6884408acc44 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Apr 29 12:07:07 2015 -0400
+++ b/tool_dependencies.xml	Thu May 14 22:47:40 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="stringtie" version="1.0.1">
-      <repository changeset_revision="2238c6c6d46a" name="package_stringtie_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  <package name="stringtie" version="1.0.3">
+      <repository changeset_revision="a98e504eb982" name="package_stringtie_1_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>