diff read_quality.xml @ 63:27e16a30667a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de

--- a/read_quality.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/read_quality.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -11,11 +11,8 @@
         -->
         <requirement type="package" version="4.2.2">r-base</requirement>
     </expand>
-
-    <expand macro="stdio" />
-
+    <expand macro="stdio"/>
     <version_command><![CDATA[read_quality.py --version]]></version_command>
-
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         read_quality.py
@@ -25,30 +22,26 @@
             --mapq ${mapq}
         ]]>
     </command>
-
     <inputs>
-        <expand macro="bam_sam_param" />
+        <expand macro="bam_sam_param"/>
         <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
-        <expand macro="mapq_param" />
-        <expand macro="rscript_output_param" />
+        <expand macro="mapq_param"/>
+        <expand macro="rscript_output_param"/>
     </inputs>
-
     <outputs>
-        <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)" />
-        <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)" />
-        <expand macro="rscript_output_data" filename="output.qual.r" />
+        <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)"/>
+        <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)"/>
+        <expand macro="rscript_output_data" filename="output.qual.r"/>
     </outputs>
-
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
-            <param name="rscript_output" value="true" />
+            <param name="rscript_output" value="true"/>
             <output name="outputr" file="output.qual_r"/>
-            <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size" />
-            <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size" />
+            <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size"/>
+            <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size"/>
         </test>
     </tests>
-
     <help><![CDATA[
 read_quality.py
 +++++++++++++++
@@ -92,7 +85,5 @@
 
 ]]>
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>