--- a/stringtie.xml	Wed Oct 21 16:07:42 2015 -0400
+++ b/stringtie.xml	Wed Jul 13 14:48:26 2016 -0400
@@ -1,38 +1,46 @@
-<tool id="stringtie" name="StringTie" version="1.1.0">
+<tool id="stringtie" name="StringTie" version="1.2.3">
     <description>transcript assembly and quantification</description>
-    <requirements>
-        <requirement type="package" version="1.1.0">stringtie</requirement>
-    </requirements>
-    <command><![CDATA[
-stringtie "$input_bam"
--o "$output_gtf"
--p "\${GALAXY_SLOTS:-1}"
-#if str($guide.use_guide) == 'yes':
-    -C "$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"
-    -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
-    #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>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+    <![CDATA[
+        #if $input_bam.metadata.ftype == 'sam':
+            samtools sort -@ \${GALAXY_SLOTS:-1} "$input_bam" | stringtie
+        #else
+            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 $guide.output_ballgown:
+                -b .
+            #end if
+        #end if
+        #if str($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
+            #if $option_set.abundance_estimation:
+                -A "$gene_abundance_estimation"
+            #end if
+            #if str($option_set.omit_sequences).strip() != "":
+                -x "$option_set.omit_sequences"
+            #end if
+        #end if
+    ]]>
+    </command>
     <inputs>
-        <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
+        <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>
@@ -40,37 +48,38 @@
             </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 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" />
             </when>
         </conditional>
         <conditional name="option_set">
-            <param label="Options" name="options" type="select">
+            <param help="" 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 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="-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" />
+                <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" />
             </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 ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
-            <filter>option_set['A']</filter>
+        <data format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
+            <filter>option_set['abundance_estimation']</filter>
         </data>
         <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
             <filter>guide['use_guide'] == "yes"</filter>
@@ -96,21 +105,21 @@
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="no" />
             <param name="options" value="default" />
-            <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
+            <output file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
         </test>
         <test>
             <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 file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
+            <output file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" 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" lines_diff="2" />
+            <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
         </test>
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
@@ -118,7 +127,7 @@
             <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" lines_diff="2" />
+            <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
         </test>
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
@@ -131,7 +140,7 @@
             <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" lines_diff="2" />
+            <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>
@@ -140,9 +149,9 @@
             <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" />
+            <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" />
         </test>
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
@@ -151,7 +160,7 @@
             <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" />
+            <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
         </test>
     </tests>
     <help>
@@ -182,18 +191,17 @@
  -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)
+ -A gene abundance estimation output file
  -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)
- -A gene abundance estimation output file
  -x do not assemble any transcripts on these reference sequence(s)
-
+ -u no multi-mapping correction default: false)
 
  ]]>
     </help>
-    <citations>
-        <citation type="doi">doi:10.1038/nbt.3122</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
+    
\ No newline at end of file