Mercurial > repos > nilesh > rseqc

changeset 61:5968573462fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author iuc
date Sat, 10 Dec 2022 11:23:05 +0000
parents 1421603cc95b
children 473382134e56
files FPKM_count.xml RNA_fragment_size.xml RPKM_saturation.xml bam2wig.xml bam_stat.xml clipping_profile.xml deletion_profile.xml geneBody_coverage.xml geneBody_coverage2.xml infer_experiment.xml inner_distance.xml insertion_profile.xml junction_annotation.xml junction_saturation.xml mismatch_profile.xml read_GC.xml read_NVC.xml read_distribution.xml read_duplication.xml read_hexamer.xml read_quality.xml rseqc_macros.xml test-data/output.splice_events.pdf test-data/output.splice_junction.pdf test-data/output.splice_junction.txt tin.xml
diffstat 26 files changed, 88 insertions(+), 59 deletions(-) [+]
line wrap: on
line diff
--- a/FPKM_count.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/FPKM_count.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,10 +1,11 @@
 <tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>calculates raw read count, FPM, and FPKM for each gene</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements" />
 
     <expand macro="stdio" />
--- a/RNA_fragment_size.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/RNA_fragment_size.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -2,10 +2,10 @@
     <description>
      calculates the fragment size for each gene/transcript
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
--- a/RPKM_saturation.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/RPKM_saturation.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,9 +1,9 @@
 <tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
--- a/bam2wig.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/bam2wig.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -2,10 +2,11 @@
     <description>
         converts all types of RNA-seq data from .bam to .wig
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
@@ -63,10 +64,10 @@
         <data format="wig" name="output" from_work_dir="outfile.wig">
             <filter>strand_type['strand_specific'] == 'none'</filter>
         </data>
-        <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)">
+        <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string}: forward reads">
             <filter>strand_type['strand_specific'] != 'none'</filter>
         </data>
-        <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)">
+        <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string}: reverse reads">
             <filter>strand_type['strand_specific'] != 'none'</filter>
         </data>
     </outputs>
--- a/bam_stat.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/bam_stat.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -2,11 +2,12 @@
     <description>
         reads mapping statistics for a provided BAM or SAM file.
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements" />
 
     <expand macro="stdio" />
@@ -25,7 +26,7 @@
     </inputs>
 
     <outputs>
-        <data format="txt" name="output" />
+        <data format="txt" name="output" label="${tool.name} on ${on_string}: stats"/>
     </outputs>
 
     <tests>
--- a/clipping_profile.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/clipping_profile.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -2,11 +2,12 @@
     <description>
      estimates clipping profile of RNA-seq reads from BAM or SAM file
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements" />
 
     <expand macro="stdio" />
@@ -27,9 +28,9 @@
     </inputs>
 
     <outputs>
-        <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" />
-        <expand macro="xls_output_data" filename="output.clipping_profile.xls" />
-        <expand macro="rscript_output_data" filename="output.clipping_profile.r" />
+        <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" label="${tool.name} on ${on_string}: PDF"/>
+        <expand macro="xls_output_data" filename="output.clipping_profile.xls" label="${tool.name} on ${on_string}: XML"/>
+        <expand macro="rscript_output_data" filename="output.clipping_profile.r" label="${tool.name} on ${on_string}: Rscript"/>
     </outputs>
 
     <tests>
--- a/deletion_profile.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/deletion_profile.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -2,11 +2,12 @@
     <description>
      calculates the distributions of deleted nucleotides across reads
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements" />
 
     <expand macro="stdio" />
--- a/geneBody_coverage.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/geneBody_coverage.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,9 +1,9 @@
 <tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>read coverage over gene body</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
@@ -50,12 +50,12 @@
   </inputs>
 
   <outputs>
-    <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves pdf)" />
-    <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap pdf)">
+    <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string}: curves (PDF)" />
+    <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string}: heatmap (PDF)">
       <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter>
     </data>
-    <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" />
-    <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" />
+    <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" label="${tool.name} on ${on_string}: Rscript"/>
+    <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string}: stats (TXT)" />
   </outputs>
 
   <!-- PDF Files contain R version, must avoid checking for diff -->
--- a/geneBody_coverage2.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/geneBody_coverage2.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,10 +1,11 @@
 <tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>read coverage over gene body</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements" />
 
     <expand macro="stdio" />
--- a/infer_experiment.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/infer_experiment.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,10 +1,11 @@
 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>speculates how RNA-seq were configured</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements" />
 
     <expand macro="stdio" />
--- a/inner_distance.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/inner_distance.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,10 +1,11 @@
 <tool id="rseqc_inner_distance" name="Inner Distance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>calculate the inner distance (or insert size) between two paired RNA reads</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements" />
 
     <expand macro="stdio" />
@@ -34,10 +35,10 @@
     </inputs>
 
     <outputs>
-        <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" />
-        <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (text)"/>
-        <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (frequency text)" />
-        <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" />
+        <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
+        <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string}: TXT"/>
+        <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string}: frequency (TXT)" />
+        <expand macro="rscript_output_data" filename="output.inner_distance_plot.r"  label="${tool.name} on ${on_string}: Rscript"/>
     </outputs>
 
     <tests>
--- a/insertion_profile.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/insertion_profile.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -2,11 +2,12 @@
     <description>
      calculates the distribution of inserted nucleotides across reads
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements" />
 
     <expand macro="stdio" />
--- a/junction_annotation.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/junction_annotation.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,10 +1,11 @@
 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>compares detected splice junctions to reference gene model</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements">
         <!--
             Required due to conda solver bug: https://github.com/conda/conda/issues/6269
@@ -25,6 +26,7 @@
             --out-prefix output
             --min-intron ${min_intron}
             --mapq ${mapq}
+        2> >(tee -a stats.txt >&2)
         ]]>
     </command>
 
@@ -37,10 +39,11 @@
     </inputs>
 
     <outputs>
-        <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events pdf)"/>
-        <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction pdf)" />
-        <expand macro="xls_output_data" filename="output.junction.xls" />
-        <expand macro="rscript_output_data" filename="output.junction_plot.r" />
+        <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/>
+        <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)" />
+        <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)" />
+        <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
+        <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats" />
     </outputs>
 
     <tests>
@@ -52,6 +55,7 @@
             <output name="outputr" file="output.junction_plot_r" />
             <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" />
             <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" />
+            <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2" />
         </test>
     </tests>
 
--- a/junction_saturation.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/junction_saturation.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,9 +1,9 @@
 <tool id="rseqc_junction_saturation" name="Junction Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>detects splice junctions from each subset and compares them to reference gene model</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <version_command><![CDATA[junction_saturation.py --version]]></version_command>
@@ -52,8 +52,8 @@
     </inputs>
 
     <outputs>
-        <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" />
-        <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" />
+        <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string}: junction saturation (PDF)"/>
+        <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string}: junction saturation (Rscript)"/>
     </outputs>
 
     <tests>
--- a/mismatch_profile.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/mismatch_profile.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -2,10 +2,10 @@
     <description>
      calculates the distribution of mismatches across reads
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
--- a/read_GC.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/read_GC.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,9 +1,9 @@
 <tool id="rseqc_read_GC" name="Read GC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>determines GC% and read count</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
@@ -27,9 +27,9 @@
     </inputs>
 
     <outputs>
-        <expand macro="pdf_output_data" filename="output.GC_plot.pdf" />
-        <expand macro="xls_output_data" filename="output.GC.xls" />
-        <expand macro="rscript_output_data" filename="output.GC_plot.r" />
+        <expand macro="pdf_output_data" filename="output.GC_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
+        <expand macro="xls_output_data" filename="output.GC.xls" label="${tool.name} on ${on_string}: XLS"/>
+        <expand macro="rscript_output_data" filename="output.GC_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
     </outputs>
 
     <tests>
--- a/read_NVC.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/read_NVC.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,9 +1,9 @@
 <tool id="rseqc_read_NVC" name="Read NVC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>to check the nucleotide composition bias</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
--- a/read_distribution.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/read_distribution.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,9 +1,9 @@
 <tool id="rseqc_read_distribution" name="Read Distribution" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>calculates how mapped reads were distributed over genome feature</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
@@ -23,7 +23,7 @@
     </inputs>
 
     <outputs>
-        <data format="txt" name="output" />
+        <data format="txt" name="output"  label="${tool.name} on ${on_string}: stats (TXT)"/>
     </outputs>
 
     <tests>
--- a/read_duplication.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/read_duplication.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,9 +1,9 @@
 <tool id="rseqc_read_duplication" name="Read Duplication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>determines reads duplication rate with sequence-based and mapping-based strategies</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
@@ -25,10 +25,10 @@
     </inputs>
 
     <outputs>
-        <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" />
-        <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position xls)"/>
-        <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence xls)"/>
-        <expand macro="rscript_output_data" filename="output.DupRate_plot.r" />
+        <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf"  label="${tool.name} on ${on_string}: plot (PDF)"/>
+        <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon (XLS)"/>
+        <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences (XLS)"/>
+        <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
     </outputs>
 
     <tests>
--- a/read_hexamer.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/read_hexamer.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -2,11 +2,10 @@
     <description>
         calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
-
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
 
     <expand macro="stdio" />
--- a/read_quality.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/read_quality.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,10 +1,9 @@
 <tool id="rseqc_read_quality" name="Read Quality" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>determines Phred quality score</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
-
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <!--
             Required due to conda solver bug: https://github.com/conda/conda/issues/6269
--- a/rseqc_macros.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/rseqc_macros.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">5.0.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@GALAXY_VERSION@">20.01</token>
     <xml name="requirements">
         <requirements>
@@ -105,16 +105,16 @@
 
     <!-- Output -->
 
-    <xml name="pdf_output_data" token_filename="output.pdf">
-        <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (pdf)" />
+    <xml name="pdf_output_data" token_filename="output.pdf" token_label="${tool.name} on ${on_string}: PDF">
+        <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="@LABEL@" />
     </xml>
 
-    <xml name="xls_output_data" token_filename="output.xls">
-        <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (xls)" />
+    <xml name="xls_output_data" token_filename="output.xls" token_label="${tool.name} on ${on_string}: XLS">
+        <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@" />
     </xml>
 
-    <xml name="rscript_output_data" token_filename="output.r">
-        <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (rscript)">
+    <xml name="rscript_output_data" token_filename="output.r" token_label="${tool.name} on ${on_string}: Rscript">
+        <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="@LABEL@">
             <filter>rscript_output</filter>
         </data>
     </xml>
Binary file test-data/output.splice_events.pdf has changed
Binary file test-data/output.splice_junction.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.splice_junction.txt	Sat Dec 10 11:23:05 2022 +0000
@@ -0,0 +1,18 @@
+Reading reference bed file:  /tmp/tmp5v623oz4/files/e/7/2/dataset_e7232361-03db-486f-9792-924d1ac24b1c.dat  ...  Done
+Load BAM file ...  Done
+
+===================================================================
+Total splicing  Events:	4
+Known Splicing Events:	1
+Partial Novel Splicing Events:	1
+Novel Splicing Events:	1
+Filtered Splicing Events:	1
+
+Total splicing  Junctions:	3
+Known Splicing Junctions:	1
+Partial Novel Splicing Junctions:	1
+Novel Splicing Junctions:	1
+
+===================================================================
+Create BED file ...
+Create Interact file ...
--- a/tin.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/tin.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -2,10 +2,10 @@
     <description>
         evaluates RNA integrity at a transcript level
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />