Mercurial > repos > iuc > comebin

changeset 3:ddfb9c10740a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit f33c09bd4b736c401cdc037e328c7be4a24d8cf5
author iuc
date Thu, 21 Aug 2025 08:48:35 +0000
parents 5910c5106cdc
children
files comebin.xml macros.xml
diffstat 2 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/comebin.xml	Mon Aug 04 11:21:41 2025 +0000
+++ b/comebin.xml	Thu Aug 21 08:48:35 2025 +0000
@@ -11,8 +11,8 @@
             
             mkdir 'outputs' 'bam_files' &&
 
-            #set $safename = re.sub('[^\w\-_\.]', '_', $assembly_file.element_identifier)
-            ln -s '$assembly_file' '${safename}.fasta' &&
+            #set $safename_fasta = re.sub('[^\w\-_\.]', '_', $assembly_file.element_identifier)
+            ln -s '$assembly_file' '${safename_fasta}.fasta' &&
 
             #for $file in $bam_files:
                 #set $safename = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
@@ -20,7 +20,7 @@
             #end for 
             
             run_comebin.sh
-            -a 'assembly_file.fasta'
+            -a '${safename_fasta}.fasta'
             -o 'outputs'
             -p 'bam_files'
             -t \${GALAXY_SLOTS:-12}
@@ -47,7 +47,7 @@
         </collection>
     </outputs>
     <tests>
-        <test expect_exit_code="1" expect_failure="true">
+        <test expect_num_outputs="1">
             <param name="assembly_file" ftype="fasta" value="input_single.fasta"/>
             <param name="bam_files" ftype="bam" value="input_single.bam"/>
             <param name="learning" value="6"/>
@@ -81,4 +81,4 @@
         ]]>
     </help>
     <expand macro="citations"/>
-</tool>
\ No newline at end of file
+</tool>
--- a/macros.xml	Mon Aug 04 11:21:41 2025 +0000
+++ b/macros.xml	Thu Aug 21 08:48:35 2025 +0000
@@ -6,7 +6,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">1.0.4</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">24.2</token>
     <xml name="citations">
         <citations>