--- a/cufflinks_wrapper.xml	Sun Feb 19 12:12:28 2017 -0500
+++ b/cufflinks_wrapper.xml	Tue Jun 16 13:00:32 2020 -0400
@@ -1,14 +1,15 @@
-<tool id="cufflinks" name="Cufflinks" version="@VERSION@.2">
+<tool id="cufflinks" name="Cufflinks" version="@VERSION@.3">
     <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description>
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
-    <version_command>cufflinks 2>&amp;1 | head -n 1</version_command>
-    <command detect_errors="aggressive">
-        python '$__tool_directory__/cufflinks_wrapper.py'
-            --input '$input'
-            --assembled-isoforms-output '$assembled_isoforms'
+    <expand macro="requirements">
+       <requirement type="package" version="3.6">python</requirement>
+    </expand>
+    <version_command><![CDATA[cufflinks 2>&1 | head -n 1]]></version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        cufflinks -q --no-update-check
+            '$input'
             --num-threads "\${GALAXY_SLOTS:-4}"
             -I $max_intron_len
             -F $min_isoform_fraction
@@ -31,30 +32,23 @@
             #if $bias_correction.do_bias_correction == "Yes":
                 -b
                 #if $bias_correction.seq_source.index_source == "history":
-                    --ref_file '$bias_correction.seq_source.ref_file'
+                    '$bias_correction.seq_source.ref_file'
                 #else:
-                    --index '${bias_correction.seq_source.index.fields.path}'
+                    '${bias_correction.seq_source.index.fields.path}'
                 #end if
             #end if
 
             ## Multi-read correct?
-            #if str($multiread_correct) == "Yes":
-                -u
-            #end if
-
-            ## Include global model if available.
-            #if $global_model:
-                --global_model '$global_model'
-            #end if
-
+            $multiread_correct
+            
             ## advanced settings
             #if $advanced_settings.use_advanced_settings == "Yes":
                 --library-type $advanced_settings.library_type
                 #if $advanced_settings.mask_file:
                     --mask-file '$advanced_settings.mask_file'
                 #end if
-                --inner-mean-dist $advanced_settings.inner_mean_dist
-                --inner-dist-std-dev $advanced_settings.inner_dist_std_dev
+                --frag-len-mean $advanced_settings.inner_mean_dist
+                --frag-len-std-dev $advanced_settings.inner_dist_std_dev
                 --max-mle-iterations $advanced_settings.max_mle_iterations
                 --junc-alpha $advanced_settings.junc_alpha
                 --small-anchor-fraction $advanced_settings.small_anchor_fraction
@@ -65,7 +59,10 @@
                 --trim-3-avgcov-thresh $advanced_settings.trim_three_avgcov_thresh
                 --trim-3-dropoff-frac $advanced_settings.trim_three_dropoff_frac
             #end if
-    </command>
+            2> stderr
+
+        && python '$__tool_directory__/mass.py' stderr '$global_model' "transcripts.gtf"
+    ]]></command>
     <inputs>
         <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
         <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help="ignore alignments with gaps longer than this"/>
@@ -125,11 +122,9 @@
             <when value="No" />
         </conditional>
 
-        <param name="multiread_correct" type="select" label="Use multi-read correct"
-            help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.">
-            <option value="No" selected="true">No</option>
-            <option value="Yes">Yes</option>
-        </param>
+        <param name="multiread_correct" type="boolean" label="Use multi-read correct"
+            truevalue="-u" falsevalue="" checked="false"
+            help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome."/>
 
         <param name="length_correction" type="select" label="Apply length correction" help="Mode of length normalization to transcript FPKM.">
             <option value="" selected="true">Cufflinks Effective Length Correction</option>
@@ -175,7 +170,7 @@
     <outputs>
         <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/>
         <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/>
-        <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/>
+        <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts" from_work_dir="transcripts.gtf"/>
         <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/>
         <data format="gtf" name="skipped" label="${tool.name} on ${on_string}: Skipped Transcripts" from_work_dir="skipped.gtf"/>
     </outputs>
@@ -200,7 +195,7 @@
             <output name="genes_expression" ftype="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/>
             <output name="transcripts_expression" ftype="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/>
             <output name="assembled_isoforms" file="cufflinks_out1.gtf"/>
-            <output name="global_model" file="cufflinks_out4.txt"/>
+            <output name="total_map_mass" file="cufflinks_out4.txt"/>
             <output name="skipped" file="cufflinks_out4.gtf"/>
         </test>
     </tests>
@@ -298,7 +293,5 @@
   -G        Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.
   -N        With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts.
     </help>
-    <citations>
-        <citation type="doi">10.1038/nbt.1621</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>