--- a/tin.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/tin.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -6,13 +6,9 @@
         <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[tin.py --version]]></version_command>
-
     <!-- Generate output files here because tin.py removes all instances of "bam"
     in the filename -->
     <command><![CDATA[
@@ -34,28 +30,17 @@
         && mv *tin.xls tin.xls
         ]]>
     </command>
-
     <inputs>
         <param name="input" type="data" format="bam" multiple="true" label="Input BAM file" help="(--input-file)"/>
-        <expand macro="refgene_param" />
-        <param name="minCov" type="integer" value="10" label="Minimum coverage (default=10)"
-            help="Minimum number of reads mapped to a transcript (--minCov)." />
-        <param name="samplesize" type="integer" value="100" label="Sample size (default=100)"
-            help="Number of equal-spaced nucleotide positions picked from mRNA.
-            Note: if this number is larger than the length of mRNA (L), it will
-            be halved until is's smaller than L. (--sample-size)." />
-        <param name="subtractbackground" type="boolean" value="false" falsevalue=""
-            truevalue="--subtract-background" label="Subtract background noise
-            (default=No)" help="Subtract background noise (estimated from
-            intronic reads). Only use this option if there are substantial
-            intronic reads (--subtract-background)." />
+        <expand macro="refgene_param"/>
+        <param name="minCov" type="integer" value="10" label="Minimum coverage (default=10)" help="Minimum number of reads mapped to a transcript (--minCov)."/>
+        <param name="samplesize" type="integer" value="100" label="Sample size (default=100)" help="Number of equal-spaced nucleotide positions picked from mRNA.             Note: if this number is larger than the length of mRNA (L), it will             be halved until is's smaller than L. (--sample-size)."/>
+        <param name="subtractbackground" type="boolean" value="false" falsevalue="" truevalue="--subtract-background" label="Subtract background noise             (default=No)" help="Subtract background noise (estimated from             intronic reads). Only use this option if there are substantial             intronic reads (--subtract-background)."/>
     </inputs>
-
     <outputs>
-        <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)" />
-        <data name="outputxls" format="tabular" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" />
+        <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)"/>
+        <data name="outputxls" format="tabular" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)"/>
     </outputs>
-
     <!-- PDF Files contain R version, must avoid checking for diff -->
     <tests>
         <test expect_num_outputs="2">
@@ -65,7 +50,6 @@
             <output name="outputxls" file="output.tin.xls" ftype="tabular"/>
         </test>
     </tests>
-
     <help><![CDATA[
 ## tin.py
 
@@ -149,7 +133,5 @@
 
 ]]>
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>