view planemo_test.sh @ 0:834843ebe569 draft

"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"

#!/bin/sh

mkdir -p planemo_test

#######################################################################################################
# TEST LA STRUCTURE
for i in *.xml
do
	echo $i
	planemo lint $i > planemo_test/`basename $i |sed 's/\.xml//'`.lint.log 2>&1
done

grep Failed planemo_test/*.lint.log

#######################################################################################################
# VALIDE L'EXECUTION
for i in ` ls *.xml | grep -vE 'demultiplexe|preprocess|clustering|remove_chimera'`
do
	echo $i
	planemo test --no_cleanup $i > planemo_test/`basename $i |sed 's/\.xml//'`.test.log 2>&1
done

grep FAILED planemo_test/*test.log


grep "test(s) executed passed" planemo_test/*test.log

# planemo_test/preprocess.test.log:All 2 test(s) executed passed.


# remote: warning: File test-data/references/01-prepro-flash.fasta is 95.81 MB; this is larger than GitHub's recommended maximum file size of 50.00 MB
# remote: error: File test-data/references/02-clustering_fastidious.fasta is 109.85 MB; this exceeds GitHub's file size limit of 100.00 MB
# remote: error: File test-data/references/01-prepro-vsearch.fasta is 121.32 MB; this exceeds GitHub's file size limit of 100.00 MB
# remote: error: File test-data/references/02-clustering_denoising.fasta is 108.50 MB; this exceeds GitHub's file size limit of 100.00 MB
# remote: error: File test-data/references/03-chimera.fasta is 109.85 MB; this exceeds GitHub's file size limit of 100.00 MB


#######################################################################################################
# TEST SOUS GALAXY

#######################################################################################################
# SOUMISSION AU TOOLSHED