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fix fly datatype (#1556)
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And linter errors that will come with the new TestsCaseValidation linter
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@bernt-matthias
bernt-matthias authored Dec 4, 2024
1 parent d9ac789 commit fb12992
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Showing 2 changed files with 25 additions and 18 deletions.
41 changes: 24 additions & 17 deletions tools/flye/flye.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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 ${on_string}: assembly graph"/>
<data name="assembly_gfa" format="gfa" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>
<data name="assembly_gfa" format="gfa1" from_work_dir="out_dir/assembly_graph.gfa" label="${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>
Expand All @@ -115,12 +115,14 @@
<!--Test 01: pacbio-raw-->
<test expect_num_outputs="5">
<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"/>
<param name="mode" value="--pacbio-raw"/>
<conditional name="mode_conditional">
<param name="mode" value="--pacbio-raw"/>
</conditional>
<param name="iterations" value="0"/>
<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="gfa" compare="diff" lines_diff="10"/>
<output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="gfa1" compare="diff" lines_diff="10"/>
<output name="consensus" ftype="fasta">
<assert_contents>
<has_line line=">contig_1"/>
Expand All @@ -131,7 +133,9 @@
<!--Test 02: nano raw-->
<test expect_num_outputs="4">
<param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
<param name="mode" value="--nano-raw"/>
<conditional name="mode_conditional">
<param name="mode" value="--nano-raw"/>
</conditional>
<param name="iterations" value="0"/>
<output name="assembly_info" ftype="tabular">
<assert_contents>
Expand All @@ -143,7 +147,7 @@
<has_size value="803" delta="100"/>
</assert_contents>
</output>
<output name="assembly_gfa" ftype="gfa">
<output name="assembly_gfa" ftype="gfa1">
<assert_contents>
<has_size value="35047" delta="100"/>
</assert_contents>
Expand All @@ -162,7 +166,7 @@
</conditional>
<conditional name="asm">
<param name="asm_select" value="true" />
<param name="asm" value="30"/>
<param name="asm_coverage" value="30"/>
<param name="genome_size" value="3980000"/>
</conditional>
<output name="assembly_info" ftype="tabular">
Expand All @@ -175,7 +179,7 @@
<has_size value="1840" delta="100"/>
</assert_contents>
</output>
<output name="assembly_gfa" ftype="gfa">
<output name="assembly_gfa" ftype="gfa1">
<assert_contents>
<has_size value="420752" delta="100"/>
</assert_contents>
Expand Down Expand Up @@ -203,7 +207,7 @@
<has_size value="367" delta="100"/>
</assert_contents>
</output>
<output name="assembly_gfa" ftype="gfa">
<output name="assembly_gfa" ftype="gfa1">
<assert_contents>
<has_size value="418729" delta="100"/>
</assert_contents>
Expand Down Expand Up @@ -231,7 +235,7 @@
<has_size value="1248" delta="100"/>
</assert_contents>
</output>
<output name="assembly_gfa" ftype="gfa">
<output name="assembly_gfa" ftype="gfa1">
<assert_contents>
<has_size value="419414" delta="1000"/>
</assert_contents>
Expand Down Expand Up @@ -260,7 +264,7 @@
<has_size value="1248" delta="500"/>
</assert_contents>
</output>
<output name="assembly_gfa" ftype="gfa">
<output name="assembly_gfa" ftype="gfa1">
<assert_contents>
<has_size value="420254" delta="2000"/>
</assert_contents>
Expand All @@ -276,10 +280,9 @@
<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"/>
<conditional name="mode_conditional">
<param name="mode" value="--pacbio-corr"/>
<param name="hifi_error" value="0.21"/>
</conditional>
<param name="min_overlap" value="1000"/>
<param name="keep-haplotypes" value="true"/>
<param name="keep_haplotypes" value="true"/>
<output name="assembly_info" ftype="tabular">
<assert_contents>
<has_size value="286" delta="200"/>
Expand All @@ -290,7 +293,7 @@
<has_size value="1273" delta="500"/>
</assert_contents>
</output>
<output name="assembly_gfa" ftype="gfa">
<output name="assembly_gfa" ftype="gfa1">
<assert_contents>
<has_size value="420254" delta="3000"/>
</assert_contents>
Expand All @@ -304,7 +307,9 @@
<!--Test 08: scaffolding mode-->
<test expect_num_outputs="4">
<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"/>
<param name="mode" value="--nano-hq"/>
<conditional name="mode_conditional">
<param name="mode" value="--nano-hq"/>
</conditional>
<param name="min_overlap" value="1000"/>
<param name="scaffold" value="true"/>
<output name="assembly_info" ftype="tabular">
Expand All @@ -317,7 +322,7 @@
<has_size value="1248" delta="100"/>
</assert_contents>
</output>
<output name="assembly_gfa" ftype="gfa">
<output name="assembly_gfa" ftype="gfa1">
<assert_contents>
<has_size value="419414" delta="2000"/>
</assert_contents>
Expand All @@ -331,7 +336,9 @@
<!--Test 09: test not-alt-contigs parameter w-->
<test expect_num_outputs="4">
<param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
<param name="mode" value="--nano-raw"/>
<conditional name="mode_conditional">
<param name="mode" value="--nano-raw"/>
</conditional>
<param name="iterations" value="0"/>
<param name="no_alt_contigs" value="true"/>
<output name="assembly_info" ftype="tabular">
Expand All @@ -344,7 +351,7 @@
<has_size value="217" delta="100"/>
</assert_contents>
</output>
<output name="assembly_gfa" ftype="gfa">
<output name="assembly_gfa" ftype="gfa1">
<assert_contents>
<has_size value="5110" delta="100"/>
</assert_contents>
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2 changes: 1 addition & 1 deletion tools/flye/macros.xml
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Original file line number Diff line number Diff line change
@@ -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>
Expand Down

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