# HG changeset patch
# User iuc
# Date 1431621029 14400
# Node ID 520e0988ec1c6abe31d094c3afc40cae81244531
# Parent  9f80c71f1779c8d3193fe076ac28845bd5e528ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a

diff -r 9f80c71f1779 -r 520e0988ec1c stringtie.xml
--- a/stringtie.xml	Thu Mar 05 11:41:12 2015 -0500
+++ b/stringtie.xml	Thu May 14 12:30:29 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 9f80c71f1779 -r 520e0988ec1c test-data/._stringtie_in1.bam
Binary file test-data/._stringtie_in1.bam has changed
diff -r 9f80c71f1779 -r 520e0988ec1c test-data/._stringtie_out2.gtf
Binary file test-data/._stringtie_out2.gtf has changed
diff -r 9f80c71f1779 -r 520e0988ec1c test-data/stringtie_out1.gtf
--- a/test-data/stringtie_out1.gtf	Thu Mar 05 11:41:12 2015 -0500
+++ b/test-data/stringtie_out1.gtf	Thu May 14 12:30:29 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 9f80c71f1779 -r 520e0988ec1c test-data/stringtie_out2.gtf
--- a/test-data/stringtie_out2.gtf	Thu Mar 05 11:41:12 2015 -0500
+++ b/test-data/stringtie_out2.gtf	Thu May 14 12:30:29 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 9f80c71f1779 -r 520e0988ec1c test-data/stringtie_out3.gtf
--- a/test-data/stringtie_out3.gtf	Thu Mar 05 11:41:12 2015 -0500
+++ b/test-data/stringtie_out3.gtf	Thu May 14 12:30:29 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 9f80c71f1779 -r 520e0988ec1c test-data/stringtie_out4.gtf
--- a/test-data/stringtie_out4.gtf	Thu Mar 05 11:41:12 2015 -0500
+++ b/test-data/stringtie_out4.gtf	Thu May 14 12:30:29 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 9f80c71f1779 -r 520e0988ec1c test-data/stringtie_out5.gtf
--- a/test-data/stringtie_out5.gtf	Thu Mar 05 11:41:12 2015 -0500
+++ b/test-data/stringtie_out5.gtf	Thu May 14 12:30:29 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";