diff junction_annotation.xml @ 13:a7f9084572fe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a

--- a/junction_annotation.xml	Sat Dec 18 19:40:16 2021 +0000
+++ b/junction_annotation.xml	Sat Dec 10 11:21:47 2022 +0000
@@ -1,16 +1,17 @@
-<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@.1">
+<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
             See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info
         -->
-        <requirement type="package" version="3.4.1">r-base</requirement>
+        <requirement type="package" version="4.2.2">r-base</requirement>
     </expand>
 
     <expand macro="stdio" />
@@ -18,12 +19,14 @@
     <version_command><![CDATA[junction_annotation.py --version]]></version_command>
 
     <command><![CDATA[
+        @BAM_SAM_INPUTS@
         junction_annotation.py
-            --input-file '${input}'
+            --input-file 'input.${extension}'
             --refgene '${refgene}'
             --out-prefix output
             --min-intron ${min_intron}
             --mapq ${mapq}
+        2> >(tee -a stats.txt >&2)
         ]]>
     </command>
 
@@ -36,10 +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>
@@ -51,6 +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>