From a648bb3309c8e810cb14efbeb39144b995ba71e6 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 4 Dec 2024 18:20:37 +0100
Subject: [PATCH] fix fly datatype

And linter errors that will come with the new TestsCaseValidation linter
---
 tools/flye/flye.xml   | 41 ++++++++++++++++++++++++-----------------
 tools/flye/macros.xml |  2 +-
 2 files changed, 25 insertions(+), 18 deletions(-)

diff --git a/tools/flye/flye.xml b/tools/flye/flye.xml
index 98ac9a2406..630745e209 100644
--- a/tools/flye/flye.xml
+++ b/tools/flye/flye.xml
@@ -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>
@@ -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"/>
@@ -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>
@@ -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>
@@ -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">
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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"/>
@@ -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>
@@ -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">
@@ -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>
@@ -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">
@@ -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>
diff --git a/tools/flye/macros.xml b/tools/flye/macros.xml
index 8fc263d9b8..2408757ede 100644
--- a/tools/flye/macros.xml
+++ b/tools/flye/macros.xml
@@ -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>