Mercurial > repos > bgruening > flye

diff flye.xml @ 12:3e4f8642c77e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
author bgruening
date Mon, 26 Aug 2024 13:54:31 +0000
parents 291923e6f276
children
line wrap: on
line diff
--- a/flye.xml	Mon Mar 18 12:44:09 2024 +0000
+++ b/flye.xml	Mon Aug 26 13:54:31 2024 +0000
@@ -105,7 +105,7 @@
     <outputs>
         <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/>
         <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/>
-        <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>
+        <data name="assembly_gfa" format="gfa" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>
         <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/>
         <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string}: log">
             <filter>generate_log</filter>
@@ -120,8 +120,12 @@
             <param name="generate_log" value="true"/>
             <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"/>
-            <output name="consensus" file="result1_assembly.fasta" ftype="fasta" compare="sim_size"/>
+            <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="gfa" compare="diff" lines_diff="10"/>
+            <output name="consensus" ftype="fasta">
+                <assert_contents>
+                    <has_line line=">contig_1"/>
+                </assert_contents>
+            </output>
             <output name="flye_log" file="result1.log" ftype="txt" compare="sim_size"/>
         </test>
         <!--Test 02: nano raw-->
@@ -139,7 +143,7 @@
                     <has_size value="803" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="txt">
+            <output name="assembly_gfa" ftype="gfa">
                 <assert_contents>
                     <has_size value="35047" delta="100"/>
                </assert_contents>
@@ -171,7 +175,7 @@
                     <has_size value="1840" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="txt">
+            <output name="assembly_gfa" ftype="gfa">
                 <assert_contents>
                     <has_size value="420752" delta="100"/>
                </assert_contents>
@@ -199,7 +203,7 @@
                     <has_size value="367" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="txt">
+            <output name="assembly_gfa" ftype="gfa">
                 <assert_contents>
                     <has_size value="418729" delta="100"/>
                </assert_contents>
@@ -227,14 +231,14 @@
                     <has_size value="1248" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="txt">
+            <output name="assembly_gfa" ftype="gfa">
                 <assert_contents>
-                    <has_size value="419414" delta="100"/>
+                    <has_size value="419414" delta="1000"/>
                </assert_contents>
             </output>
             <output name="consensus" ftype="fasta">
                 <assert_contents>
-                    <has_size value="426277" delta="100"/>
+                    <has_size value="426277" delta="1000"/>
                </assert_contents>
             </output>
         </test>
@@ -253,17 +257,17 @@
             </output>
             <output name="assembly_graph" ftype="graph_dot">
                 <assert_contents>
-                    <has_size value="1500" delta="100"/>
+                    <has_size value="1248" delta="500"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="txt">
+            <output name="assembly_gfa" ftype="gfa">
                 <assert_contents>
-                    <has_size value="418422" delta="100"/>
+                    <has_size value="420254" delta="2000"/>
                </assert_contents>
             </output>
             <output name="consensus" ftype="fasta">
                 <assert_contents>
-                    <has_size value="425147" delta="200"/>
+                    <has_size value="427131" delta="2000"/>
                </assert_contents>
             </output>
         </test>
@@ -278,22 +282,22 @@
             <param name="keep-haplotypes" value="true"/>
             <output name="assembly_info" ftype="tabular">
                 <assert_contents>
-                    <has_size value="286" delta="100"/>
+                    <has_size value="286" delta="200"/>
                </assert_contents>
             </output>
             <output name="assembly_graph" ftype="graph_dot">
                 <assert_contents>
-                    <has_size value="1273" delta="100"/>
+                    <has_size value="1273" delta="500"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="txt">
+            <output name="assembly_gfa" ftype="gfa">
                 <assert_contents>
-                    <has_size value="418511" delta="100"/>
+                    <has_size value="420254" delta="3000"/>
                </assert_contents>
             </output>
             <output name="consensus" ftype="fasta">
                 <assert_contents>
-                    <has_size value="425267" delta="100"/>
+                    <has_size value="427131" delta="3000"/>
                </assert_contents>
             </output>
         </test>
@@ -313,14 +317,14 @@
                     <has_size value="1248" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="txt">
+            <output name="assembly_gfa" ftype="gfa">
                 <assert_contents>
-                    <has_size value="419414" delta="1000"/>
+                    <has_size value="419414" delta="2000"/>
                </assert_contents>
             </output>
             <output name="consensus" ftype="fasta">
                 <assert_contents>
-                    <has_size value="426277" delta="1000"/>
+                    <has_size value="426277" delta="2000"/>
                </assert_contents>
             </output>
         </test>
@@ -340,7 +344,7 @@
                     <has_size value="217" delta="100"/>
                </assert_contents>
             </output>
-            <output name="assembly_gfa" ftype="txt">
+            <output name="assembly_gfa" ftype="gfa">
                 <assert_contents>
                     <has_size value="5110" delta="100"/>
                </assert_contents>