diff bin.xml @ 2:1bd3c93f565f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b

--- a/bin.xml	Mon Mar 27 08:21:46 2023 +0000
+++ b/bin.xml	Tue Mar 25 15:51:24 2025 +0000
@@ -11,7 +11,7 @@
     <command detect_errors="exit_code"><![CDATA[
 #import re
 @FASTA_FILES@
-SemiBin bin
+SemiBin2 bin
     --input-fasta 'contigs.fasta'
     --data '$data'
 #if $mod.select == 'history'
@@ -22,10 +22,13 @@
     --output 'output'
     --threads \${GALAXY_SLOTS:-1}
     --minfasta-kbs $minfasta_kbs
-    $no_recluster
+#if $mode.select == 'single' or $mode_fasta.mode_select == 'co'
+    $write_pre_reclustering_bins
+#end if
     --max-node $max_node
     --max-edges $max_edges
     --random-seed $random_seed
+    --compression none
     @MIN_LEN@
     --orf-finder '$orf_finder'
     ]]></command>
@@ -50,20 +53,20 @@
         <expand macro="max-node"/>
         <expand macro="max-edges"/>
         <expand macro="minfasta-kbs"/>
-        <expand macro="no-recluster"/>
+        <expand macro="write_pre_reclustering_bins"/>
     </inputs>
     <outputs>
-        <collection name="output_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">
-            <filter>not no_recluster</filter>
-            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins" />
+        <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">
+            <filter>not write_pre_reclustering_bins</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins" />
         </collection>
-        <collection name="output_prerecluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
-            <filter>not no_recluster</filter>
-            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_prerecluster_bins" />
+        <collection name="output_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reclustered bins?">
+            <filter>write_pre_reclustering_bins</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins" />
         </collection>
-        <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins without reeclustering">
-            <filter>no_recluster</filter>
-            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins" />
+        <collection name="output_prerecluster_bins" type="list" label="${tool.name} on ${on_string}: Pre reclustered bins">
+            <filter>write_pre_reclustering_bins</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_prerecluster_bins" />
         </collection>
     </outputs>
     <tests>
@@ -82,26 +85,25 @@
                 <param name="min_len" value="0" />
             </conditional>
             <param name="orf_finder" value="prodigal"/>
-            <param name="random-seed" value="0"/>
+            <param name="random_seed" value="0"/>
             <param name="max_node" value="1"/>
             <param name="max_edges" value="200"/>
             <param name="minfasta_kbs" value="200"/>
-            <param name="no_recluster" value="false"/>
-            <output_collection name="output_recluster_bins" count="0"/>
+            <param name="write_pre_reclustering_bins" value="true"/>
             <output_collection name="output_prerecluster_bins" count="3">
-                <element name="0" ftype="fasta">
+                <element name="SemiBin_0" ftype="fasta">
                     <assert_contents>
                         <has_text text=">g1k_0"/>
                         <has_text text=">g4k_9"/>
                     </assert_contents>
                 </element>
-                <element name="1" ftype="fasta">
+                <element name="SemiBin_1" ftype="fasta">
                     <assert_contents>
                         <has_text text=">g2k_0"/>
                         <has_text text=">g2k_9"/>
                     </assert_contents>
                 </element>
-                <element name="2" ftype="fasta">
+                <element name="SemiBin_2" ftype="fasta">
                     <assert_contents>
                         <has_text text=">g3k_0"/>
                         <has_text text=">g3k_9"/>
@@ -124,31 +126,34 @@
                 <param name="min_len" value="0" />
             </conditional>
             <param name="orf_finder" value="prodigal"/>
-            <param name="random-seed" value="0"/>
+            <param name="random_seed" value="0"/>
             <param name="max_node" value="1"/>
             <param name="max_edges" value="200"/>
             <param name="minfasta_kbs" value="200"/>
-            <param name="no_recluster" value="true"/>
-            <output_collection name="output_bins" count="3">
-                <element name="0" ftype="fasta">
-                    <assert_contents>
-                        <has_text text=">g1k_0"/>
-                        <has_text text=">g4k_9"/>
-                    </assert_contents>
-                </element>
-                <element name="1" ftype="fasta">
-                    <assert_contents>
-                        <has_text text=">g2k_0"/>
-                        <has_text text=">g2k_9"/>
-                    </assert_contents>
-                </element>
-                <element name="2" ftype="fasta">
-                    <assert_contents>
-                        <has_text text=">g3k_0"/>
-                        <has_text text=">g3k_9"/>
-                    </assert_contents>
-                </element>
-            </output_collection>
+            <param name="write_pre_reclustering_bins" value="false"/>
+            <output_collection name="output_bins" count="0"/>
+        </test>
+        <test expect_num_outputs="2">
+            <conditional name="mode">
+                <param name="select" value="single"/>
+                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+            </conditional>
+            <param name="data" ftype="csv" value="data.csv"/>
+            <conditional name="mod">
+                <param name="select" value="history"/>
+                <param name="model" ftype="h5" value="model.h5"/>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="min-len"/>
+                <param name="min_len" value="0" />
+            </conditional>
+            <param name="orf_finder" value="prodigal"/>
+            <param name="random_seed" value="0"/>
+            <param name="max_node" value="1"/>
+            <param name="max_edges" value="200"/>
+            <param name="minfasta_kbs" value="200"/>
+            <param name="write_pre_reclustering_bins" value="true"/>
+            <output_collection name="output_prerecluster_bins" count="3"/>
         </test>
     </tests>
     <help><![CDATA[