diff maxbin2.xml @ 7:28a0b1446d2b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit be3f3d0eb7e565cea414babb410e6ae32875c5f2

--- a/maxbin2.xml	Mon Oct 16 07:46:13 2023 +0000
+++ b/maxbin2.xml	Wed Dec 20 20:27:57 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy4">
+<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy5">
     <description>clusters metagenomic contigs into bins</description>
     <macros>
         <token name="@MAXBIN_VERSION@">2.2.7</token>
@@ -30,7 +30,7 @@
     #if $assembly.type == 'individual'
         ## uncompress .gz reads files if necessary
         #set $e = $assembly.inputs.reads
-        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
+        #set $identifier = re.sub('[^\w\-\\.]', '_', str($e.element_identifier))
         #if $e.ext.endswith(".gz")
 gunzip -c '$e' > '$identifier' &&
 echo '$identifier' >> reads_list &&
@@ -394,6 +394,38 @@
             <output name="noclass" file="4/out.noclass" ftype="fasta" />
             <output name="toshort" file="4/out.tooshort" ftype="fasta" />
         </test>
+        <!-- test w contigs and reads in fastqsanger format as input (and whitespace in reads filename)-->
+        <test expect_num_outputs="4">
+            <param name="contig" value="test4_contigs.fasta" ftype="fasta" />
+            <conditional name="assembly">
+                <param name="type" value="individual"/>
+                <conditional name="inputs">
+                    <param name="type" value="reads"/>
+                    <param name="reads" value="test4_reads 2.fastqsanger" ftype="fastqsanger"/>
+                    <param name="output_abundances" value="false"/>
+                    <param name="reassembly" value=""/>
+                </conditional>
+            </conditional>
+            <section name="adv">
+                <param name="min_contig_length" value="1000"/>
+                <param name="max_iteration" value="50"/>
+                <param name="prob_threshold" value="0.5"/>
+            </section>
+            <section name="output">
+                <param name="plotmarker" value=""/>
+                <param name="marker" value="false"/>
+                <param name="markers" value="false" />
+                <param name="log" value="false"/>
+                <param name="markerset" value="107"/>
+            </section>
+            <output_collection name="bins" type="list" count="2">
+                <element name="001" file="4/out.001.fasta" ftype="fasta"/>
+                <element name="002" file="4/out.002.fasta" ftype="fasta"/>
+            </output_collection>
+            <output name="summary" file="4/out.summary" ftype="tabular" />
+            <output name="noclass" file="4/out.noclass" ftype="fasta" />
+            <output name="toshort" file="4/out.tooshort" ftype="fasta" />
+        </test>
         <!-- test w contigs and reads in fastqsanger.gz format as input -->
         <test expect_num_outputs="4">
             <param name="contig" value="test4_contigs.fasta" ftype="fasta" />