--- a/stringtie.xml	Thu Jul 03 18:38:02 2014 -0400
+++ b/stringtie.xml	Thu Mar 05 11:41:12 2015 -0500
@@ -1,19 +1,20 @@
-<?xml version="1.0"?>
-<tool name="StringTie" id="stringtie" version="1.0.0">
+<tool id="stringtie" name="StringTie" version="1.0.1">
     <description>RNA-Seq assembler</description>
     <requirements>
-        <requirement type="package" version="0.97">stringtie</requirement>
+        <requirement type="package" version="1.0.1">stringtie</requirement>
     </requirements>
-    <command>
-<![CDATA[
+    <command><![CDATA[
 stringtie "$input_bam"
 -o "$output_gtf"
 -p "\${GALAXY_SLOTS:-1}"
 #if str($guide.use_guide) == 'yes':
-    -G "$guide.guide_gff" $guide.input_estimation
-    -C "$coverage"
+    -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
+    #if str($guide.output_ballgown) == '-b':
+        $guide.output_ballgown `pwd`
+    #end if
 #end if
 #if str($option_set.options) == 'advanced':
+    -l "$option_set.name_prefix"
     -f "$option_set.fraction"
     -m "$option_set.min_tlen"
     -a "$option_set.min_anchor_len"
@@ -26,92 +27,142 @@
 ]]>
 </command>
     <inputs>
-        <param name="input_bam" type="data" format="bam" label="BAM file to assemble" />
+        <param format="bam" label="BAM file to assemble" name="input_bam" type="data" />
         <conditional name="guide">
-            <param name="use_guide" type="select" label="Use GFF file to guide assembly">
+            <param label="Use GFF file to guide assembly" name="use_guide" type="select">
                 <option value="yes">Use GFF</option>
-                <option value="no" selected="True">Do not use GFF</option>
+                <option selected="True" value="no">Do not use GFF</option>
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="guide_gff" type="data" format="gtf,gff3" label="Reference annotation to use for guiding the assembly process" />
-                <param name="input_estimation" type="boolean" truevalue="-e" falsevalue="" label="Perform abundance estimation only of input transcripts" />
+                <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">
-            <param name="options" type="select" label="Options">
-                <option value="default" selected="True">Use defaults</option>
+            <param label="Options" name="options" type="select">
+                <option selected="True" value="default">Use defaults</option>
                 <option value="advanced">Specify advanced options</option>
             </param>
             <when value="default" />
             <when value="advanced">
-                <param name="disable_trimming" type="boolean" falsevalue="" truevalue="-t" label="Disable trimming of predicted transcripts based on coverage" />
-                <param name="sensitive" type="boolean" truevalue="-S" falsevalue="" label="Increase sensitivity" />
-                <param name="label" type="text" value="STRG" label="Name prefix for output transcripts" />
-                <param name="fraction" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" />
-                <param name="min_tlen" type="integer" value="200" label="Minimum assembled transcript length" />
-                <param name="min_anchor_len" type="integer" value="10" label="Minimum anchor length for junctions" />
-                <param name="min_anchor_cov" type="integer" value="1" label="Minimum junction coverage" />
-                <param name="min_bundle_cov" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" />
-                <param name="maxcov" type="integer" value="1000000" label="Coverage saturation threshold" />
-                <param name="bdist" type="integer" value="50" label="Gap between read mappings triggering a new bundle" />
-                <param name="bundle_fraction" type="float" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" />
-             </when>
+                <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>
     <outputs>
-        <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts"/>
-        <data name="coverage" format="gff3" label="${tool.name} on ${on_string}: Coverage">
+        <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
+        <data format="gff3" label="${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 ${on_string}: exon-level expression measurements" name="exon_expression">
+            <filter>guide['output_ballgown']</filter>
+        </data>
+        <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
+            <filter>guide['output_ballgown']</filter>
+        </data>
+        <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
+            <filter>guide['output_ballgown']</filter>
+        </data>
+        <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
+            <filter>guide['output_ballgown']</filter>
+        </data>
+        <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
+            <filter>guide['output_ballgown']</filter>
+        </data>
     </outputs>
     <tests>
         <test>
-            <param name="input_bam" value="stringtie_in1.bam" ftype="bam" />
+            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="no" />
             <param name="options" value="default" />
-            <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" />
+            <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" />
         </test>
         <test>
-            <param name="input_bam" value="stringtie_in1.bam" ftype="bam" />
+            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="no" />
             <param name="options" value="advanced" />
             <param name="fraction" value="0.17" />
-            <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" />
+            <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" />
+        </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="default" />
+            <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" />
+        </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" />
+            <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" />
+        </test>
+        <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="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="stringtie_out5.gtf" ftype="gtf" name="output_gtf" />
+            <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
         </test>
     </tests>
     <help>
 <![CDATA[
-StringTie v0.97 usage::
-
-   stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gff>] [-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>]
-
-  Assemble RNA-Seq alignments into potential transcripts.
+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]
 
-   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: 0.15)
-   -m  minimum assembled transcript length to report (default 200bp)
-   -o  output file with the assembled transcripts (default: stdout)
-   -a  minimum anchor length for junctions (default: 10)
-   -j  minimum junction coverage (default: 1)
-   -t  disable trimming of predicted transcripts based on coverage (default: trimming enabled)
-   -c  minimum bundle reads per bp coverage to consider for assembly (default: 2)
-   -s  coverage saturation threshold; further read alignments will be
-       ignored in a region where a local coverage depth of <maxcov>
-       is reached (default: 1,000,000);
-   -v  verbose (log bundle processing details)
-   -e  abundance estimation only of input transcripts (for -G option)
-   -g  gap between read mappings triggering a new bundle (default: 50)
-   -S  more sensitive run (default: no)
-   -C  output file with all transcripts in reference that are fully
-       covered by reads
-   -M  fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
-   -p  number of threads (CPUs) to use (default: 1)
-
-]]>
-</help>
-</tool>
\ No newline at end of file
+Assemble RNA-Seq alignments into potential transcripts.
+ 
+ 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)
+ -m minimum assembled transcript length to report (default 200bp)
+ -o output path/file name for the assembled transcripts GTF (default: stdout)
+ -a minimum anchor length for junctions (default: 10)
+ -j minimum junction coverage (default: 1)
+ -t disable trimming of predicted transcripts based on coverage
+    (default: coverage trimming is enabled)
+ -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)
+ -s coverage saturation threshold; further read alignments will be
+    ignored in a region where a local coverage depth of <maxcov> 
+    is reached (default: 1,000,000);
+ -v verbose (log bundle processing details)
+ -g gap between read mappings triggering a new bundle (default: 50)
+ -C output file with reference transcripts that are covered by reads
+ -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
+ -p number of threads (CPUs) to use (default: 1)
+ -B enable output of Ballgown table files which will be created in the
+    same directory as the output GTF (requires -G, -o recommended)
+ -b enable output of Ballgown table files but these files will be 
+    created under the directory path given as <dir_path>
+ -e only estimates the abundance of given reference transcripts (requires -G)
+ ]]>
+    </help>
+    <citations>
+        <citation type="doi">doi:10.1038/nbt.3122</citation>
+    </citations>
+</tool>