changeset 4:7d997332582e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit b32e3a4bfaf7e014097eeb0b850b61bac218802d

--- a/das_tool.xml	Thu Jul 06 12:27:11 2023 +0000
+++ b/das_tool.xml	Sun Feb 25 11:28:02 2024 +0000
@@ -1,7 +1,5 @@
 <tool id="das_tool" name="DAS Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>
-        for genome resolved metagenomics
-    </description>
+    <description>for genome-resolved metagenomics</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -19,7 +17,7 @@
 #end for
 
 #if $adv.proteins
-ln -s $adv.proteins 'proteins' &&
+    ln -s '$adv.proteins' 'proteins' &&
 #end if
 
 DAS_Tool
@@ -28,17 +26,19 @@
     --bins '$bins'
     --labels '$labels'
     --search_engine '$adv.search_engine'
-#if $adv.proteins
-    --proteins 'proteins'
-#end if
+    #if $adv.proteins
+        --proteins 'proteins'
+    #end if
     --score_threshold $adv.score_threshold
     --duplicate_penalty $adv.duplicate_penalty
     --megabin_penalty $adv.megabin_penalty
+    --max_iter_post_threshold $adv.max_iter_post_threshold
+
     $output.write_bin_evals
     $output.write_bins.write_bins
-#if str($output.write_bins.write_bins) != ''
-    $output.write_bins.write_unbinned
-#end if
+    #if str($output.write_bins.write_bins) != ''
+        $output.write_bins.write_unbinned
+    #end if
     $output.debug
     --threads \${GALAXY_SLOTS:-1}
     ]]></command>
@@ -57,6 +57,7 @@
             <param argument="--score_threshold" type="float" min="0" max="1" value="0.5" label="Score threshold until selection algorithm will keep selecting bins"/>
             <param argument="--duplicate_penalty" type="float" min="0" max="3" value="0.6" label="Penalty for duplicate single copy genes per bin (weight b)" help="Only change if you know what you are doing"/>
             <param argument="--megabin_penalty" type="float" min="0" max="3" value="0.5" label="Penalty for megabins (weight c)" help="Only change if you know what you are doing"/>
+            <param argument="--max_iter_post_threshold" type="integer" min="1" value="10" label="Maximum number of iterations after reaching score threshold"/>
         </section>
         <section name="output" title="Outputs">
             <param name="proteins" type="boolean" checked="false" label="Output predicted proteins?"/>
@@ -202,7 +203,7 @@
 Inputs
 ======
 
-- Bins: Tab separated files of contig-IDs and bin-IDs. Contigs to bin file example: ::
+- Bins: Tab-separated files of contig-IDs and bin-IDs. Contigs to bin file example: ::
 
     Contig_1	bin.01
     Contig_8	bin.01
@@ -216,7 +217,7 @@
     >Contig_2
     GATCGTCACGCAGGCTATCGGAGCCTCGACCCGCAAGCTCTGCGCCTTGGAGCAGG...
 
-- [Optional] Proteins: Predicted proteins in prodigal fasta format. Header contains contig-ID and gene number: ::
+- [Optional] Proteins: Predicted proteins in prodigal fasta format. The header contains contig-ID and gene number: ::
 
     >Contig_1_1
     MPRKNKKLPRHLLVIRTSAMGDVAMLPHALRALKEAYPEVKVTVATKSLFHPFFEG...

--- a/macros.xml	Thu Jul 06 12:27:11 2023 +0000
+++ b/macros.xml	Sun Feb 25 11:28:02 2024 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.1.6</token>
+    <token name="@TOOL_VERSION@">1.1.7</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">