Mercurial > repos > bgruening > flye

diff flye.xml @ 2:156e0da5b917 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit a926a92aed3e22b14fb88af204c8450987c59743
author bgruening
date Thu, 29 Nov 2018 04:34:34 -0500
parents cd256484eb1a
children 1ce9b1d72ec3
line wrap: on
line diff
--- a/flye.xml	Fri Sep 28 19:18:54 2018 -0400
+++ b/flye.xml	Thu Nov 29 04:34:34 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="flye" name="Assembly" version="2.3.5">
+<tool id="flye" name="Assembly" version="2.3.7">
     <description>of long and error-prone reads</description>
     <macros>
         <import>macros.xml</import>
@@ -25,7 +25,7 @@
     flye
     $mode
     #for $counter, $input in enumerate($inputs):
-        ./input_${counter}.${input.ext}
+        ./input_${counter}.$ext
     #end for
 
     -o out_dir 
@@ -61,30 +61,30 @@
     </outputs>
     <tests>
         <test>            
-            <param name="inputs" ftype="fasta" value="E.coli_PacBio_40x_first_200_reads.fasta"/>
+            <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
             <param name="mode" value="--pacbio-raw"/>
-            <param name="g" value="1m"/>
-            <output name="contigs" file="result1_contigs.fasta" ftype="fasta"/>
-            <output name="scaffolds" file="result1_scaffolds.fasta" ftype="fasta"/>
-            <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular"/>
+            <param name="g" value="10000"/>
+            <output name="contigs" file="result1_contigs.fasta" ftype="fasta" compare="sim_size"/>
+            <output name="scaffolds" file="result1_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
+            <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"/>    
         </test>
         <test>            
-            <param name="inputs" ftype="fasta" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
+            <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
             <param name="mode" value="--nano-raw"/>
-            <param name="g" value="100000"/>
-            <output name="contigs" file="result2_contigs.fasta" ftype="fasta"/>
-            <output name="scaffolds" file="result2_scaffolds.fasta" ftype="fasta"/>
-            <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular"/>
+            <param name="g" value="10000"/>
+            <output name="contigs" file="result2_contigs.fasta" ftype="fasta" compare="sim_size"/>
+            <output name="scaffolds" file="result2_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
+            <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"/>    
         </test>
         <test>            
-            <param name="inputs" ftype="fasta" value="E.coli_PacBio_40x_first_200_reads.fasta"/>
+            <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
             <param name="mode" value="--pacbio-raw"/>
-            <param name="g" value="1.1m"/>
+            <param name="g" value="10000"/>
             <param name="i" value="2"/>
-            <output name="contigs" file="result3_contigs.fasta" ftype="fasta"/>
-            <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta"/>
+            <output name="contigs" file="result3_contigs.fasta" ftype="fasta" compare="sim_size"/>
+            <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[