diff flye.xml @ 6:0284be52bfcf draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"

--- a/flye.xml	Mon Nov 02 17:54:14 2020 +0000
+++ b/flye.xml	Thu Jan 14 11:19:21 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="flye" name="Flye assembly" version="2.6+galaxy0">
+<tool id="flye" name="Flye assembly" version="2.8.2+galaxy0">
     <description>of long and error-prone reads</description>
     <macros>
         <import>macros.xml</import>
@@ -29,14 +29,14 @@
     #end for
 
     -o out_dir
-    -g '$g'
     -t \${GALAXY_SLOTS:-4}
     -i $i
     #if $m:
         -m '$m'
     #end if
-    #if $asm:
-        --asm-coverage '$asm'
+    #if str($asm.asm_select) == "true":
+        --asm-coverage '$asm.asm'
+        -g '$asm.g'
     #end if
     ${plasmids}
     ${meta}
@@ -52,12 +52,23 @@
             <option value="--pacbio-corr">PacBio corrected</option>
             <option value="--subassemblies">high-quality contig-like input</option>
         </param>
-        <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)">
-            <validator type="regex" message="Genome size must be a float  or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
-        </param>
         <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
         <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" />
-        <param name="asm" argument="--asm-coverage" type="integer" optional="true" label="reduced coverage for initial disjointing assembly" />
+
+        <conditional name="asm">
+            <param name="asm_select" type="select" label="description" help="">
+                <option value="true">Enable reduced coverage for initial disjointing assembly</option>
+                <option value="false" selected="true">Disable reduced coverage for initial disjointing assembly</option>
+            </param>
+            <when value="true">
+                <param name="asm" argument="--asm-coverage" type="integer" label="reduced coverage for initial disjointing assembly" />
+                <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)">
+                    <validator type="regex" message="Genome size must be a float  or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
+                </param>
+            </when>
+            <when value="false" />
+        </conditional>
+
         <param argument="--plasmids" type="boolean" truevalue="--plasmids" falsevalue="" checked="False" label="rescue short unassembled plasmids" />
         <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="perform metagenomic assembly" />
         <param name="no_trestle" argument="--no-trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip trestle stage" />
@@ -73,7 +84,6 @@
         <test>
             <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
             <param name="mode" value="--pacbio-raw"/>
-            <param name="g" value="10000"/>
             <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
             <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
             <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
@@ -82,7 +92,6 @@
         <test>
             <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
             <param name="mode" value="--nano-raw"/>
-            <param name="g" value="10000"/>
             <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular" compare="sim_size"/>
             <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
             <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
@@ -91,9 +100,12 @@
         <test>
             <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
             <param name="mode" value="--nano-corr"/>
-            <param name="g" value="10000"/>
             <param name="i" value="2"/>
-            <param name="asm" value="40"/>
+            <conditional name="asm">
+                <param name="asm_select" value="true" />
+                <param name="asm" value="40"/>
+                <param name="g" value="10000"/>
+            </conditional>
             <output name="assembly_info" file="result3_assembly_info.txt" ftype="tabular" compare="sim_size"/>
             <output name="assembly_graph" file="result3_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
             <output name="assembly_gfa" file="result3_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
@@ -102,7 +114,6 @@
         <test>
             <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
             <param name="mode" value="--pacbio-raw"/>
-            <param name="g" value="10000"/>
             <param name="i" value="1"/>
             <param name="meta" value="true"/>
             <param name="plasmids" value="true"/>