tools/tests/Makefile, tools/tests/should-get-tests/*: update paths

See #3039.

tools/tests/Makefile

-SHOULD=$(wildcard *.should-get)
+SHOULD=$(wildcard should-get-tests/*.should-get)
 TAP=$(SHOULD:.should-get=.tap)
 
 all: $(TAP) doctests
 
-fuse-doc.tap: fuse-doc.should-get force
+should-get-tests/fuse-doc.tap: should-get-tests/fuse-doc.should-get force
 	$(MAKE) -C ../../doc analysis-example1.vidjil
 	../should-to-tap.sh $<
 

tools/tests/should-get-tests/diff-two-files-c.should-get

-!LAUNCH: python ../diff.py ../../algo/tests/data/results-two-clones-1-2.vidjil ../../algo/tests/data/results-two-clones-1-3.vidjil -c
+!LAUNCH: python ../../diff.py ../../../algo/tests/data/results-two-clones-1-2.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil -c
 
 $ Clone id-1 is a common clone, with a different number of reads 
 1:id-1 .* 800 .* 300

tools/tests/should-get-tests/diff-two-files.should-get

-!LAUNCH: python ../diff.py ../../algo/tests/data/results-two-clones-1-2.vidjil ../../algo/tests/data/results-two-clones-1-3.vidjil
+!LAUNCH: python ../../diff.py ../../../algo/tests/data/results-two-clones-1-2.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil
 
 $ Clone id-1 has a different number of reads 
 1:Not the same number or reads: id-1

tools/tests/should-get-tests/fuse-doc.should-get

-!LAUNCH: python ../fuse.py ../../doc/analysis-example1.vidjil ../../doc/analysis-example2.vidjil; cat fused.vidjil | python ../format_json.py -1 -u
+!LAUNCH: python ../../fuse.py ../../../doc/analysis-example1.vidjil ../../../doc/analysis-example2.vidjil; cat fused.vidjil | python ../../format_json.py -1 -u
 
 $ Fuse the two examples (three samples, two identical)
 e1:"segmented": [335662, 335662, 410124]

tools/tests/should-get-tests/fuse-files-no-clones.should-get

-!LAUNCH: python ../fuse.py ../../algo/tests/data/no_clones.vidjil ../../algo/tests/data/results-two-clones-1-2.vidjil -o fused_no_clones.vidjil; cat fused_no_clones.vidjil
+!LAUNCH: python ../../fuse.py ../../../algo/tests/data/no_clones.vidjil ../../../algo/tests/data/results-two-clones-1-2.vidjil -o fused_no_clones.vidjil; cat fused_no_clones.vidjil
 
 $ Fuse the three files
 2: ListWindows: .0, 1000.

tools/tests/should-get-tests/fuse-three-files.should-get

-!LAUNCH: python ../fuse.py ../../algo/tests/data/results-two-clones-1-2.vidjil ../../algo/tests/data/results-two-clones-1-2.vidjil ../../algo/tests/data/results-two-clones-1-2.vidjil ; cat fused.vidjil
+!LAUNCH: python ../../fuse.py ../../../algo/tests/data/results-two-clones-1-2.vidjil ../../../algo/tests/data/results-two-clones-1-2.vidjil ../../../algo/tests/data/results-two-clones-1-2.vidjil ; cat fused.vidjil
 
 $ Fuse the three files
 2: ListWindows: .1000, 1000, 1000.

tools/tests/should-get-tests/latex.should-get

-!LAUNCH: python ../latex.py ../../algo/tests/data/results-two-clones-1-2.vidjil 
+!LAUNCH: python ../../latex.py ../../../algo/tests/data/results-two-clones-1-2.vidjil 
 
 $ Display the name of the .vidjil file
 2: data/results-two-clones-1-2.vidjil

tools/tests/should-get-tests/vidjil-to-fasta-with-sequences.should-get

-!LAUNCH: (cd ..; python vidjil-to-fasta.py -o tests/vidjil-to-fasta-with-sequences.fasta ../doc/analysis-example.vidjil > /dev/null; cat tests/vidjil-to-fasta-with-sequences.fasta)
+!LAUNCH: python ../../vidjil-to-fasta.py -o vidjil-to-fasta-with-sequences.fasta ../../../doc/analysis-example.vidjil > /dev/null; cat vidjil-to-fasta-with-sequences.fasta
 
 $ 19 sequences with a seg field should be found
 19:^>

tools/tests/should-get-tests/vidjil-to-fasta.should-get

-!LAUNCH: (cd ..; python vidjil-to-fasta.py -o tests/vidjil-to-fasta.fasta ../data/no_clones.vidjil > /dev/null; cat tests/vidjil-to-fasta.fasta)
+!LAUNCH: python ../../vidjil-to-fasta.py -o vidjil-to-fasta.fasta ../../../data/no_clones.vidjil > /dev/null; cat vidjil-to-fasta.fasta
 
 $ No data should be found
 0:.

tools/tests/should-get-tests/window-change.should-get

-!LAUNCH: (cd .. ; python analysis-windows.py -w 40 ../algo/tests/data/analysis-with-windows.analysis ; python analysis-windows.py -w 60 ../algo/tests/data/analysis-with-windows.analysis.new ; ./diff_json.sh ../algo/tests/data/analysis-with-windows.analysis{,.new.new} -s ; cat ../algo/tests/data/analysis-with-windows.analysis.new)
+!LAUNCH: (cd ../.. ; python analysis-windows.py -w 40 ../algo/tests/data/analysis-with-windows.analysis ; python analysis-windows.py -w 60 ../algo/tests/data/analysis-with-windows.analysis.new ; ./diff_json.sh ../algo/tests/data/analysis-with-windows.analysis{,.new.new} -s ; cat ../algo/tests/data/analysis-with-windows.analysis.new)
 
 $ First and last files are identical
 1:are identical