# HG changeset patch
# User artbio
# Date 1696989572 0
# Node ID 320f7746b9f5193620d9b1209094e918d03be252
# Parent  1997af8f46483a285dd4da0e36e1fbf0e863e983
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse commit d520bdab019f9afc3f78912bfbd174909114da4f

diff -r 1997af8f4648 -r 320f7746b9f5 bamparse.xml
--- a/bamparse.xml	Thu Jul 20 00:32:36 2023 +0000
+++ b/bamparse.xml	Wed Oct 11 01:59:32 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="bamparse" name="Count alignments" version="4.1.0">
+<tool id="bamparse" name="Count alignments" version="4.1.1">
     <description>in a BAM file</description>
     <requirements>
             <requirement type="package" version="0.21.0=py310h41dec4a_1">pysam</requirement>
@@ -67,7 +67,7 @@
             <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
             <param name="polarity" value="both" />
             <param name="output_option" value="unique" />
-            <output name="table" ftype="tabular" file="table.tabular" count="1"/>
+            <output name="table" ftype="tabular" file="table.tabular" />
         </test>
         <test expect_num_outputs="1">
             <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
@@ -82,13 +82,13 @@
             <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
             <param name="polarity" value="sense" />
             <param name="output_option" value="unique" />
-            <output name="table" ftype="tabular" file="table.tabular" count="1"/>
+            <output name="table" ftype="tabular" file="table.tabular" />
         </test>
         <test expect_num_outputs="1">
             <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
             <param name="polarity" value="antisense" />
             <param name="output_option" value="unique" />
-            <output name="table" ftype="tabular" file="table_antisense.tabular" count="1"/>
+            <output name="table" ftype="tabular" file="table_antisense.tabular" />
         </test>
 
         <test expect_num_outputs="1">
@@ -105,13 +105,13 @@
             <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
             <param name="polarity" value="sense" />
             <param name="output_option" value="unique" />
-            <output name="table" ftype="tabular" file="more_sense_table.tabular" count="1"/>
+            <output name="table" ftype="tabular" file="more_sense_table.tabular" />
         </test>
         <test expect_num_outputs="1">
             <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
             <param name="polarity" value="antisense" />
             <param name="output_option" value="unique" />
-            <output name="table" ftype="tabular" file="more_antisense_table.tabular" count="1"/>
+            <output name="table" ftype="tabular" file="more_antisense_table.tabular" />
         </test>
     </tests>
     <help>
@@ -126,4 +126,7 @@
 The library labels in the returned count table are taken from the input bam datasets
 names in the Galaxy history.
     </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp352</citation>
+    </citations>
 </tool>