# HG changeset patch
# User artbio
# Date 1696551575 0
# Node ID ac8ea1ca115db6dbf8a687699224c1e966aad32e
# Parent  ee2fbee916f7412b8737e66c2a18689c8d839475
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig commit 85bdb086a4aa403465844a0b10399440b31b65a7

diff -r ee2fbee916f7 -r ac8ea1ca115d bigwig_to_wig.sh
--- a/bigwig_to_wig.sh	Tue Sep 25 17:41:20 2018 -0400
+++ b/bigwig_to_wig.sh	Fri Oct 06 00:19:35 2023 +0000
@@ -54,22 +54,22 @@
 
 #for each chromsome
 while read line; do
- 
-  cur_chr=$(echo $line | cut --delimiter=" " -f1)
-  cur_length=$(echo $line | cut --delimiter=" " -f2)
-  
+
+  cur_chr=$(echo $line | cut -d " " -f1)
+  cur_length=$(echo $line | cut -d " " -f2)
+
   n_bins=$(echo "scale=0; (${cur_length}-${step_size})/${bin_size}" | bc)
- 
+
   start=1
   stop=$(echo "$n_bins * $bin_size" | bc)
 
   #write header line for each chromosome
   echo "fixedStep chrom=$cur_chr start=$start step=$step_size span=$step_size"
-  
+
   #get densities along chr in n_bins with chosen bin_size and step_size (giving overlap in bins)
   nice bigWigSummary $bigwig_file $cur_chr $start $stop $n_bins | perl -pe 's/\t/\n/g' | perl -pe "s/n\/a/0/" 
   #gives warning if no data in/for current chromosome
-  
+
 done < $org_assembly_file
 
 #rm tmp
diff -r ee2fbee916f7 -r ac8ea1ca115d bigwig_to_wig.xml
--- a/bigwig_to_wig.xml	Tue Sep 25 17:41:20 2018 -0400
+++ b/bigwig_to_wig.xml	Fri Oct 06 00:19:35 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="bigwig_to_wig" name="BigWig to Wig" version="2.0.0">
+<tool id="bigwig_to_wig" name="BigWig to Wig" version="@VERSION@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,7 @@
         <exit_code range="1:" level="fatal" description="Tool exception" />
     </stdio>
     <command detect_errors="exit_code"><![CDATA[
-        sh $__tool_directory__/bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output
+        bash $__tool_directory__/bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output
     ]]></command>
   <inputs>
       <param name="input" format="bigwig" type="data" label="BigWig file to convert" />
@@ -23,13 +23,13 @@
 	      <param name="input" value="1.bigwig" />
 	      <param name="bin_size" value="500" />
 	      <param name="mylab" value="wiggle_file" />
-	      <output name="output" file="1.wig" />	  
+	      <output name="output" file="1.wig" compare="sim_size" />	  
       </test>
       <test>
 	      <param name="input" value="2.bigwig" />
 	      <param name="bin_size" value="2000" />
 	      <param name="mylab" value="wiggle_file" />
-	      <output name="output" file="2.wig" />	  
+	      <output name="output" file="2.wig" compare="sim_size" />	  
       </test>
     </tests>
     <help><![CDATA[
diff -r ee2fbee916f7 -r ac8ea1ca115d macros.xml
--- a/macros.xml	Tue Sep 25 17:41:20 2018 -0400
+++ b/macros.xml	Fri Oct 06 00:19:35 2023 +0000
@@ -1,10 +1,11 @@
 <macros>
-    <token name="@VERSION@">2.0.0</token>
+    <token name="@VERSION@">3+galaxy0</token>
     <macro name="requirements">
     <requirements>
-        <requirement type="package" version="366">ucsc-bigwiginfo</requirement>
-        <requirement type="package" version="366">ucsc-bigwigsummary</requirement>
-        <requirement type="package" version="1.06">bc</requirement>
+        <requirement type="package" version="377">ucsc-bigwiginfo</requirement>
+        <requirement type="package" version="377">ucsc-bigwigsummary</requirement>
+        <requirement type="package" version="1.07.1">bc</requirement>
+        <requirement type="package" version="5.32.1">perl</requirement>
     </requirements>
     </macro>
 
@@ -33,15 +34,10 @@
 
 **Credits**
 
-This tool is based on the script written by Jens Vilstrup Johansen and is an update of a Galaxy tool previously developed by nikos_.
-
-It uses bigWigInfo_ and bigWigSummary_.
-
-For support and bug reports contact Cedric Mendoza or Christophe Antoniewski or go to https://github.com/ARTbio/tools-artbio
+This tool is based on the script written by Jens Vilstrup Johansen and is an update
+of a Galaxy tool previously developed by nikos_.
 
 .. _nikos: https://toolshed.g2.bx.psu.edu/view/nikos/bigwig_to_wig/974af3268394
-.. _bigWigInfo: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigInfo
-.. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary
 
     </token>
 </macros>