From 123be432644b0c83c28766e5ebdbe3988acec096 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Mon, 28 Mar 2022 14:34:25 +0200
Subject: [PATCH] test plans workflow
---
test-plans.snakefile | 17 +++++++++++++++++
test.plan | 11 ++++++++---
2 files changed, 25 insertions(+), 3 deletions(-)
create mode 100644 test-plans.snakefile
diff --git a/test-plans.snakefile b/test-plans.snakefile
new file mode 100644
index 0000000..74e5425
--- /dev/null
+++ b/test-plans.snakefile
@@ -0,0 +1,17 @@
+configfile: 'config.yaml'
+
+
+rule all:
+ input:
+ config['OUTDIR'] + '/compare.txt',
+
+
+rule test_plans:
+ output:
+ config['OUTDIR'] + '/compare.txt'
+
+ input:
+ 'test.plan'
+
+ shell:
+ '''{config[ALVISNLP]} -param compare outFile {output} {input} && tail -n 9 output/compare.txt | [ $(\grep -F -c 100.00) = "6" ]'''
diff --git a/test.plan b/test.plan
index 5c87994..2140721 100644
--- a/test.plan
+++ b/test.plan
@@ -14,9 +14,14 @@
<name>microorganisms-taxids</name>
</select-microorganisms-taxids>
- <select-microorganisms-taxroots href="select-taxa.plan">
+ <select-microorganisms-taxpaths href="select-taxa.plan">
<list>output/microorganisms-roots-paths.txt</list>
<name>microorganisms-taxroots</name>
- <mode>taxroots</mode>
- </select-microorganisms-taxroots>
+ <mode>taxpaths</mode>
+ </select-microorganisms-taxpaths>
+
+ <compare class="LayerComparator">
+ <predictedLayerName>microorganisms-taxroots</predictedLayerName>
+ <referenceLayerName>microorganisms-taxids</referenceLayerName>
+ </compare>
</alvisnlp-plan>
--
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