diff concatenate_fasta.xml @ 6:a72b974c98a2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6

--- a/concatenate_fasta.xml	Sun Aug 10 11:38:22 2025 +0000
+++ b/concatenate_fasta.xml	Tue Oct 28 08:21:31 2025 +0000
@@ -11,23 +11,23 @@
     <command detect_errors="exit_code"><![CDATA[
 #import re
 #for $e in $input_fasta
-    #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
-    #if $e.ext.endswith(".gz")
-gunzip -c '$e' > '${identifier}.fasta' &&
-    #else
-ln -s '$e' '${identifier}.fasta' &&
-    #end if
+    #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
+    ln -s '$e' '${identifier}.$e.ext' &&
 #end for
 
 SemiBin2 concatenate_fasta
-    --input-fasta *.fasta
+    --input-fasta
+    #for $e in $input_fasta
+        #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
+            '${identifier}.$e.ext'
+    #end for
     --output 'output'
     --separator '$separator'
     --compression none
     -m $min_len
     ]]></command>
     <inputs>
-        <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/>
+        <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz,fasta.bz2" label="Contig sequences"/>
         <expand macro="separator"/>
         <expand macro="concat_min_len"/>
     </inputs>
@@ -41,9 +41,9 @@
             <param name="min_len" value="0"/>
             <output name="fasta" ftype="fasta">
                 <assert_contents>
-                    <has_text text=">input_single:g1k_0"/>
-                    <has_text text=">input_single_3:g4k_7"/>
-                    <has_text text=">input_single_2:g1k_0"/>
+                    <has_text text=">input_single_fasta:g1k_0"/>
+                    <has_text text=">input_single_3_fasta:g4k_7"/>
+                    <has_text text=">input_single_2_fasta:g1k_0"/>
                 </assert_contents>
             </output>
         </test>