--- a/tin.xml	Sat Dec 18 19:41:19 2021 +0000
+++ b/tin.xml	Sat Nov 26 15:19:14 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="rseqc_tin" name="Transcript Integrity Number" version="@TOOL_VERSION@.1">
+<tool id="rseqc_tin" name="Transcript Integrity Number" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>
         evaluates RNA integrity at a transcript level
     </description>
@@ -17,15 +17,26 @@
     in the filename -->
     <command><![CDATA[
         #import re
-        ln -sf '${input}' 'input.bam' &&
-        ln -sf '${input.metadata.bam_index}' 'input.bam.bai' &&
-        tin.py -i 'input.bam' --refgene='${refgene}' --minCov=${minCov}
+        #set $input_list = []
+        #for $i, $input in enumerate($input):
+            #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
+            #if $safename in $input_list:
+                #set $safename = str($safename) + "." + str($i)
+            #end if
+            $input_list.append($safename)
+            ln -sf '${input}' '${safename}.bam' &&
+            ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' &&
+            echo '${safename}.bam' >> 'input_list.txt' &&
+        #end for
+        tin.py -i 'input_list.txt' --refgene='${refgene}' --minCov=${minCov}
         --sample-size=${samplesize} ${subtractbackground}
+        && mv *summary.txt summary.tab
+        && mv *tin.xls tin.xls
         ]]>
     </command>
 
     <inputs>
-        <expand macro="bam_param" />
+        <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)." />
@@ -41,22 +52,17 @@
     </inputs>
 
     <outputs>
-        <data name="outputsummary" format="tabular" from_work_dir="input.summary.txt" label="TIN on ${on_string} (summary)" />
-        <data name="outputxls" format="xls" from_work_dir="input.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="xls" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" />
     </outputs>
 
     <!-- PDF Files contain R version, must avoid checking for diff -->
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
-            <output name="outputsummary">
-                <assert_contents>
-                    <has_line_matching expression="^Bam_file\tTIN\(mean\)\tTIN\(median\)\tTIN\(stdev\)$" />
-                    <has_line_matching expression="^input\.bam\t8\.8709677419\d+\t8\.8709677419\d+\t0\.0$" />
-                </assert_contents>
-            </output>
-            <output name="outputxls" file="output.tin.xls"/>
+            <output name="outputsummary" file="summary.tin.txt" ftype="tabular"/>
+            <output name="outputxls" file="output.tin.xls" ftype="xls"/>
         </test>
     </tests>