| Previous changeset 13:1f0769f0b56b (2024-09-18) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit fb1299282c85caf05328489921813aefdf83ff26 |
|
modified:
flye.xml macros.xml |
| b |
| diff -r 1f0769f0b56b -r cd11366d92cf flye.xml --- a/flye.xml Wed Sep 18 16:43:00 2024 +0000 +++ b/flye.xml Wed Dec 04 22:12:50 2024 +0000 |
| b |
| b'@@ -105,7 +105,7 @@\n <outputs>\n <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/>\n <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/>\n- <data name="assembly_gfa" format="gfa" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>\n+ <data name="assembly_gfa" format="gfa1" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>\n <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/>\n <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string}: log">\n <filter>generate_log</filter>\n@@ -115,12 +115,14 @@\n <!--Test 01: pacbio-raw-->\n <test expect_num_outputs="5">\n <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/>\n- <param name="mode" value="--pacbio-raw"/>\n+ <conditional name="mode_conditional">\n+ <param name="mode" value="--pacbio-raw"/>\n+ </conditional>\n <param name="iterations" value="0"/>\n <param name="generate_log" value="true"/>\n <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>\n <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>\n- <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="gfa" compare="diff" lines_diff="10"/>\n+ <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="gfa1" compare="diff" lines_diff="10"/>\n <output name="consensus" ftype="fasta">\n <assert_contents>\n <has_line line=">contig_1"/>\n@@ -131,7 +133,9 @@\n <!--Test 02: nano raw-->\n <test expect_num_outputs="4">\n <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>\n- <param name="mode" value="--nano-raw"/>\n+ <conditional name="mode_conditional">\n+ <param name="mode" value="--nano-raw"/>\n+ </conditional>\n <param name="iterations" value="0"/>\n <output name="assembly_info" ftype="tabular">\n <assert_contents>\n@@ -143,7 +147,7 @@\n <has_size value="803" delta="100"/>\n </assert_contents>\n </output>\n- <output name="assembly_gfa" ftype="gfa">\n+ <output name="assembly_gfa" ftype="gfa1">\n <assert_contents>\n <has_size value="35047" delta="100"/>\n </assert_contents>\n@@ -162,7 +166,7 @@\n </conditional>\n <conditional name="asm">\n <param name="asm_select" value="true" />\n- <param name="asm" value="30"/>\n+ <param name="asm_coverage" value="30"/>\n <param name="genome_size" value="3980000"/>\n </conditional>\n <output name="assembly_info" ftype="tabular">\n@@ -175,7 +179,7 @@\n <has_size value="1840" delta="100"/>\n </assert_contents>\n </output>\n- <output name="assembly_gfa" ftype="gfa">\n+ <output name="assembly_gfa" ftype="gfa1">\n <assert_contents>\n <has_size value="420752" delta="100"/>\n </assert_contents>\n@@ -203,7 +207,7 @@\n <has_size value="367" delta="100"/>\n </assert_contents>\n </output>\n- <output name="assembly_gfa" ftype="gfa">\n+ <ou'..b'ta="100"/>\n </assert_contents>\n@@ -231,7 +235,7 @@\n <has_size value="1248" delta="100"/>\n </assert_contents>\n </output>\n- <output name="assembly_gfa" ftype="gfa">\n+ <output name="assembly_gfa" ftype="gfa1">\n <assert_contents>\n <has_size value="419414" delta="1000"/>\n </assert_contents>\n@@ -260,7 +264,7 @@\n <has_size value="1248" delta="500"/>\n </assert_contents>\n </output>\n- <output name="assembly_gfa" ftype="gfa">\n+ <output name="assembly_gfa" ftype="gfa1">\n <assert_contents>\n <has_size value="420254" delta="2000"/>\n </assert_contents>\n@@ -276,10 +280,9 @@\n <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>\n <conditional name="mode_conditional">\n <param name="mode" value="--pacbio-corr"/>\n- <param name="hifi_error" value="0.21"/>\n </conditional>\n <param name="min_overlap" value="1000"/>\n- <param name="keep-haplotypes" value="true"/>\n+ <param name="keep_haplotypes" value="true"/>\n <output name="assembly_info" ftype="tabular">\n <assert_contents>\n <has_size value="286" delta="200"/>\n@@ -290,7 +293,7 @@\n <has_size value="1273" delta="500"/>\n </assert_contents>\n </output>\n- <output name="assembly_gfa" ftype="gfa">\n+ <output name="assembly_gfa" ftype="gfa1">\n <assert_contents>\n <has_size value="420254" delta="3000"/>\n </assert_contents>\n@@ -304,7 +307,9 @@\n <!--Test 08: scaffolding mode-->\n <test expect_num_outputs="4">\n <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>\n- <param name="mode" value="--nano-hq"/>\n+ <conditional name="mode_conditional">\n+ <param name="mode" value="--nano-hq"/>\n+ </conditional>\n <param name="min_overlap" value="1000"/>\n <param name="scaffold" value="true"/>\n <output name="assembly_info" ftype="tabular">\n@@ -317,7 +322,7 @@\n <has_size value="1248" delta="100"/>\n </assert_contents>\n </output>\n- <output name="assembly_gfa" ftype="gfa">\n+ <output name="assembly_gfa" ftype="gfa1">\n <assert_contents>\n <has_size value="419414" delta="2000"/>\n </assert_contents>\n@@ -331,7 +336,9 @@\n <!--Test 09: test not-alt-contigs parameter w-->\n <test expect_num_outputs="4">\n <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>\n- <param name="mode" value="--nano-raw"/>\n+ <conditional name="mode_conditional">\n+ <param name="mode" value="--nano-raw"/>\n+ </conditional>\n <param name="iterations" value="0"/>\n <param name="no_alt_contigs" value="true"/>\n <output name="assembly_info" ftype="tabular">\n@@ -344,7 +351,7 @@\n <has_size value="217" delta="100"/>\n </assert_contents>\n </output>\n- <output name="assembly_gfa" ftype="gfa">\n+ <output name="assembly_gfa" ftype="gfa1">\n <assert_contents>\n <has_size value="5110" delta="100"/>\n </assert_contents>\n' |
| b |
| diff -r 1f0769f0b56b -r cd11366d92cf macros.xml --- a/macros.xml Wed Sep 18 16:43:00 2024 +0000 +++ b/macros.xml Wed Dec 04 22:12:50 2024 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.9.5</token> - <token name="@SUFFIX_VERSION@">0</token> + <token name="@SUFFIX_VERSION@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">flye</requirement> |