Mercurial > repos > nilesh > rseqc

diff mismatch_profile.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/mismatch_profile.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/mismatch_profile.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -6,44 +6,36 @@
         <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[mismatch_profile.py --version]]></version_command>
-
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         mismatch_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq}
         ]]>
     </command>
-
     <inputs>
-        <expand macro="bam_param" />
-        <expand macro="readlength_param" />
-        <expand macro="readnum_param" />
-        <expand macro="mapq_param" />
-        <expand macro="rscript_output_param" />
+        <expand macro="bam_param"/>
+        <expand macro="readlength_param"/>
+        <expand macro="readnum_param"/>
+        <expand macro="mapq_param"/>
+        <expand macro="rscript_output_param"/>
     </inputs>
-
     <outputs>
-        <expand macro="pdf_output_data" filename="output.mismatch_profile.pdf" />
-        <expand macro="xls_output_data" filename="output.mismatch_profile.xls" />
-        <expand macro="rscript_output_data" filename="output.mismatch_profile.r" />
+        <expand macro="pdf_output_data" filename="output.mismatch_profile.pdf"/>
+        <expand macro="xls_output_data" filename="output.mismatch_profile.xls"/>
+        <expand macro="rscript_output_data" filename="output.mismatch_profile.r"/>
     </outputs>
-
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
-            <param name="read_align_length" value="101" />
-            <param name="rscript_output" value="true" />
-            <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size" />
+            <param name="read_align_length" value="101"/>
+            <param name="rscript_output" value="true"/>
+            <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size"/>
             <output name="outputxls" file="output.mismatch_profile.xls" ftype="tabular"/>
             <output name="outputr" file="output.mismatch_profile_r"/>
         </test>
     </tests>
-
     <help><![CDATA[
 mismatch_profile.py
 +++++++++++++++++++
@@ -84,7 +76,5 @@
 ]]>
 
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>