Mercurial > repos > iuc > semibin_generate_cannot_links

diff generate_cannot_links.xml @ 2:1f458611f27e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
author iuc
date Tue, 25 Mar 2025 15:50:29 +0000
parents 40dfbeb5bc41
children 46f144cf132d
line wrap: on
line diff
--- a/generate_cannot_links.xml	Mon Mar 27 08:23:44 2023 +0000
+++ b/generate_cannot_links.xml	Tue Mar 25 15:50:29 2025 +0000
@@ -11,18 +11,19 @@
     <command detect_errors="exit_code"><![CDATA[
 #import re
 @FASTA_FILES@
-SemiBin
+SemiBin2
     generate_cannot_links
     --input-fasta 'contigs.fasta'
     --output 'output'
     --cannot-name 'cannot'
 #if $mode.ref.select == "cached"
     --reference-db-data-dir '$mode.ref.cached_db.fields.path'
-#else
+#end if
+#if $mode.ref.select == "taxonomy"
     --taxonomy-annotation-table '$mode.ref.taxonomy_annotation_table'
 #end if
     @MIN_LEN@
-#if str($ml_threshold) != ''
+#if $ml_threshold:
     --ml-threshold $ml_threshold
 #end if
     --cannot-name 'cannot'
@@ -34,15 +35,15 @@
             <expand macro="mode_select"/>
             <when value="single">
                 <expand macro="input-fasta-single"/>
-                <expand macro="ref-single"/>
+                <expand macro="ref-single-cannot"/>
             </when>
             <when value="co">
                 <expand macro="input-fasta-single"/>
-                <expand macro="ref-single"/>
+                <expand macro="ref-single-cannot"/>
             </when>
             <when value="multi">
                 <expand macro="input-fasta-multi"/>
-                <expand macro="ref-multi"/>
+                <expand macro="ref-multi-cannot"/>
             </when>
         </conditional>
         <expand macro="min_len"/>
@@ -65,7 +66,6 @@
                 <param name="method" value="min-len"/>
                 <param name="min_len" value="0" />
             </conditional>
-            <param name="ml_threshold" value=""/>
             <output name="cannot" ftype="txt">
                 <assert_contents>
                     <has_text text="g1k_0,g4k_0"/>
@@ -87,7 +87,6 @@
                 <param name="method" value="min-len"/>
                 <param name="min_len" value="0" />
             </conditional>
-            <param name="ml_threshold" value=""/>
             <output name="cannot" ftype="txt">
                 <assert_contents>
                     <has_text text="g1k_0,g4k_0"/>
@@ -101,7 +100,7 @@
                 <param name="select" value="single"/>
                 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
                 <conditional name="ref">
-                    <param name="db_selector" value="cached"/>
+                    <param name="select" value="cached"/>
                     <param name="cached_db" value="test-db"/>
                 </conditional>
             </conditional>
@@ -109,11 +108,9 @@
                 <param name="method" value="min-len"/>
                 <param name="min_len" value="0" />
             </conditional>
-            <param name="ml_threshold" value=""/>
             <output name="cannot" ftype="txt">
                 <assert_contents>
-                    <has_text text="g1k_0,g2k_0"/>
-                    <has_text text="g2k_9,g4k_1"/>
+                    <has_n_lines n='300' delta="10"/>
                 </assert_contents>
             </output>
         </test>