Mercurial > repos > iuc > bedtools

diff shuffleBed.xml @ 47:2892111d91f8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:40:09 +0000
parents 64e2edfe7a2c
children
line wrap: on
line diff
--- a/shuffleBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/shuffleBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>randomly redistrubute intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
@@ -11,8 +11,8 @@
 @GENOME_FILE@
 -i '$inputA'
 $bedpe
-#if str($seed.seed_choose) == "True":
-    -seed $seed.seed
+#if str($seed) != "":
+    -seed $seed
 #end if
 #if str($add_bed.add_bed_select) == "not_be":
     -excl $add_bed.excl
@@ -68,40 +68,36 @@
     <tests>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="shuffleBed.len" ftype="tabular" />
-            <param name="chrom" value="" />
-            <param name="seed_choose" value="True" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" />
+            <param name="chrom" value="false" />
             <param name="seed" value="1" />
             <output name="output" file="shuffleBed_result1.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="shuffleBed.len" ftype="tabular" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" />
             <param name="chrom" value="True" />
-            <param name="seed_choose" value="True" />
             <param name="seed" value="1" />
             <output name="output" file="shuffleBed_result2.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="shuffleBed.len" ftype="tabular" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" />
             <conditional name="add_bed">
                 <param name="add_bed_select" value="not_be"/>
                 <param name="excl" value="shuffleBed2.bed" ftype="bed" />
             </conditional>
-            <param name="seed_choose" value="True" />
             <param name="seed" value="1" />
             <output name="output" file="shuffleBed_result3.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="shuffleBed.len" ftype="bed" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="bed" />
             <param name="allow_beyond" value="True" />
-            <param name="seed_choose" value="True" />
             <param name="seed" value="3" />
             <output name="output" file="shuffleBed_result4.bed" ftype="bed" />
         </test>