--- a/stringtie.xml	Wed Aug 12 07:07:40 2015 -0400
+++ b/stringtie.xml	Wed Oct 21 16:07:42 2015 -0400
@@ -1,7 +1,7 @@
-<tool id="stringtie" name="StringTie" version="1.0.4">
+<tool id="stringtie" name="StringTie" version="1.1.0">
     <description>transcript assembly and quantification</description>
     <requirements>
-        <requirement type="package" version="1.0.4">stringtie</requirement>
+        <requirement type="package" version="1.1.0">stringtie</requirement>
     </requirements>
     <command><![CDATA[
 stringtie "$input_bam"
@@ -20,9 +20,14 @@
     -a "$option_set.min_anchor_len"
     -j "$option_set.min_anchor_cov"
     -c "$option_set.min_bundle_cov"
-    -s "$option_set.maxcov"
     -g "$option_set.bdist"
     -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
+    #if $option_set.A:
+        -A "$gene_abundance_estimation"
+    #end if
+    #if str($option_set.x).strip() != "":
+        -x "$option_set.x"
+    #end if
 #end if
 ]]>
 </command>
@@ -55,14 +60,18 @@
                 <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 argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="e.g. chrM,chrX" />
+                <param argument="-A" truevalue="-A" falsevalue="" type="boolean" help="" label="Additional gene abundance estimation output file" />
             </when>
         </conditional>
     </inputs>
     <outputs>
         <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
+        <data format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
+            <filter>option_set['A']</filter>
+        </data>
         <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
             <filter>guide['use_guide'] == "yes"</filter>
         </data>
@@ -125,6 +134,25 @@
             <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
             <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="A" value="True" />
+            <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
+            <output file="stringtie_out6.gtf" ftype="tabular" name="gene_abundance_estimation" />
+        </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="0.15" />
+            <param name="c" value="test_chromosome" />
+            <output file="stringtie_out7.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
+        </test>
     </tests>
     <help>
 <![CDATA[
@@ -142,16 +170,13 @@
  -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)
+ -m minimum assembled transcript length (default: 200)
  -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
@@ -162,6 +187,10 @@
  -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)
+ -A gene abundance estimation output file
+ -x do not assemble any transcripts on these reference sequence(s)
+
+
  ]]>
     </help>
     <citations>