Mercurial > repos > bgruening > flye
diff flye.xml @ 12:3e4f8642c77e draft
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 |
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--- 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>