Mercurial > repos > iuc > semibin_generate_cannot_links

diff generate_cannot_links.xml @ 6:fd17362def4f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
author iuc
date Tue, 28 Oct 2025 08:19:11 +0000
parents 68d2cd0be567
children
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--- a/generate_cannot_links.xml	Sun Aug 10 11:39:20 2025 +0000
+++ b/generate_cannot_links.xml	Tue Oct 28 08:19:11 2025 +0000
@@ -13,7 +13,11 @@
 @FASTA_FILES@
 SemiBin2
     generate_cannot_links
-    --input-fasta 'contigs.fasta'
+#if $mode.select == 'single' or $mode.select == 'co'
+    --input-fasta 'contigs.$input_fasta.ext'
+#else
+    --input_fasta 'contigs.fasta'
+#end if
     --output 'output'
     --cannot-name 'cannot'
 #if $mode.ref.select == "cached"
@@ -56,7 +60,7 @@
         <test expect_num_outputs="1">
             <conditional name="mode">
                 <param name="select" value="single"/>
-                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                <param name="input_fasta" ftype="fasta.gz" value="input_single.fasta.gz"/>
                 <conditional name="ref">
                     <param name="select" value="taxonomy"/>
                     <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
@@ -77,7 +81,7 @@
         <test expect_num_outputs="1">
             <conditional name="mode">
                 <param name="select" value="single"/>
-                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                <param name="input_fasta" ftype="fasta.bz2" value="input_single.fasta.bz2"/>
                 <conditional name="ref">
                     <param name="select" value="taxonomy"/>
                     <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>