Mercurial > repos > nilesh > rseqc

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

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 473382134e56
children
line wrap: on
line diff
--- a/read_GC.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/read_GC.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -4,13 +4,9 @@
         <import>rseqc_macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
-
-    <expand macro="requirements" />
-
-    <expand macro="stdio" />
-
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <version_command><![CDATA[read_GC.py --version]]></version_command>
-
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         read_GC.py
@@ -19,29 +15,25 @@
             --mapq ${mapq}
         ]]>
     </command>
-
     <inputs>
-        <expand macro="bam_sam_param" />
-        <expand macro="mapq_param" />
-        <expand macro="rscript_output_param" />
+        <expand macro="bam_sam_param"/>
+        <expand macro="mapq_param"/>
+        <expand macro="rscript_output_param"/>
     </inputs>
-
     <outputs>
         <expand macro="pdf_output_data" filename="output.GC_plot.pdf" label="${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>
-        <test>
-            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
-            <param name="rscript_output" value="true" />
+        <test expect_num_outputs="3">
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="rscript_output" value="true"/>
             <output name="outputxls" file="output.GC.xls" ftype="tabular"/>
-            <output name="outputr" file="output.GC_plot_r" />
-            <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size" />
+            <output name="outputr" file="output.GC_plot_r"/>
+            <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size"/>
         </test>
     </tests>
-
     <help><![CDATA[
 read_GC.py
 ++++++++++
@@ -69,7 +61,5 @@
 
 ]]>
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>