Manifests can point at local test-data folders now

As of #149, each tool has its own test-data/ folder
(currently a symlink to the top level shared folder).
This means the manifest no longer needs to point at
the top level folder.

$ sed -i.bak "s#../../test-data/#test-data/#g" tools/*/.shed.yml

Author: peterjc

tools/blast2go/.shed.yml

@@ -22,8 +22,8 @@ type: unrestricted
 include:
 - strip_components: 2
   source:
-  - ../../test-data/blastp_sample.blast2go.tabular
-  - ../../test-data/blastp_sample.xml
+  - test-data/blastp_sample.blast2go.tabular
+  - test-data/blastp_sample.xml
   - ../../tool-data/blast2go.loc.sample
   - ../../tools/blast2go/README.rst
   - ../../tools/blast2go/blast2go.py

tools/blast_rbh/.shed.yml

@@ -13,19 +13,19 @@ type: unrestricted
 include:
 - strip_components: 2
   source:
-  - ../../test-data/four_human_proteins.fasta
-  - ../../test-data/k12_edited_proteins.fasta
-  - ../../test-data/k12_ten_proteins.fasta
-  - ../../test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular
-  - ../../test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular
-  - ../../test-data/rbh_blastp_k12.tabular
-  - ../../test-data/rbh_blastp_k12_self.tabular
-  - ../../test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular
-  - ../../test-data/rbh_none.tabular
-  - ../../test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular
-  - ../../test-data/rhodopsin_nucs.fasta
-  - ../../test-data/rhodopsin_proteins.fasta
-  - ../../test-data/three_human_mRNA.fasta
+  - test-data/four_human_proteins.fasta
+  - test-data/k12_edited_proteins.fasta
+  - test-data/k12_ten_proteins.fasta
+  - test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular
+  - test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular
+  - test-data/rbh_blastp_k12.tabular
+  - test-data/rbh_blastp_k12_self.tabular
+  - test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular
+  - test-data/rbh_none.tabular
+  - test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular
+  - test-data/rhodopsin_nucs.fasta
+  - test-data/rhodopsin_proteins.fasta
+  - test-data/three_human_mRNA.fasta
   - ../../tools/blast_rbh/README.rst
   - ../../tools/blast_rbh/best_hits.py
   - ../../tools/blast_rbh/blast_rbh.py

tools/blastxml_to_top_descr/.shed.yml

@@ -27,10 +27,10 @@ type: unrestricted
 include:
 - strip_components: 2
   source:
-  - ../../test-data/blastp_four_human_vs_rhodopsin.xml
-  - ../../test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular
-  - ../../test-data/blastp_four_human_vs_rhodopsin_top3.tabular
-  - ../../test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular
+  - test-data/blastp_four_human_vs_rhodopsin.xml
+  - test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular
+  - test-data/blastp_four_human_vs_rhodopsin_top3.tabular
+  - test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular
   - ../../tools/blastxml_to_top_descr/README.rst
   - ../../tools/blastxml_to_top_descr/blastxml_to_top_descr.py
   - ../../tools/blastxml_to_top_descr/blastxml_to_top_descr.xml

tools/make_nr/.shed.yml

@@ -18,10 +18,10 @@ include:
   - ../../tools/make_nr/README.rst
   - ../../tools/make_nr/make_nr.py
   - ../../tools/make_nr/make_nr.xml
-  - ../../test-data/duplicates.fasta
-  - ../../test-data/duplicates.fasta.gz
-  - ../../test-data/duplicates.nr.fasta
-  - ../../test-data/more_duplicates.fasta
-  - ../../test-data/deduplicate.nosortids.fasta
-  - ../../test-data/deduplicate.sortids.fasta
-  - ../../test-data/empty.fasta
+  - test-data/duplicates.fasta
+  - test-data/duplicates.fasta.gz
+  - test-data/duplicates.nr.fasta
+  - test-data/more_duplicates.fasta
+  - test-data/deduplicate.nosortids.fasta
+  - test-data/deduplicate.sortids.fasta
+  - test-data/empty.fasta

tools/ncbi_blast_plus/.shed.yml

@@ -13,120 +13,120 @@ type: unrestricted
 include:
 - strip_components: 2
   source:
-  - ../../test-data/blastdb.loc
-  - ../../test-data/blastdb_d.loc
-  - ../../test-data/blastdb_p.loc
-  - ../../test-data/blastn_arabidopsis.extended.tabular
-  - ../../test-data/blastn_arabidopsis.standard.tabular
-  - ../../test-data/blastn_arabidopsis.xml
-  - ../../test-data/blastn_chimera_vs_three_human_max1.tabular
-  - ../../test-data/blastn_chimera_vs_three_human_max1.txt
-  - ../../test-data/blastn_rhodopsin_vs_three_human.columns.tabular
-  - ../../test-data/blastn_rhodopsin_vs_three_human.tabular
-  - ../../test-data/blastn_rhodopsin_vs_three_human.xml
-  - ../../test-data/blastn_rhodopsin_vs_three_human_converted.tabular
-  - ../../test-data/blastn_chimera_vs_three_human_db.tabular
-  - ../../test-data/blastn_chimera_vs_rhodopsin_db.tabular
-  - ../../test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular
-  - ../../test-data/blastp_four_human_vs_rhodopsin.tabular
-  - ../../test-data/blastp_four_human_vs_rhodopsin.xml
-  - ../../test-data/blastp_four_human_vs_rhodopsin_converted.tabular
-  - ../../test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular
-  - ../../test-data/blastp_four_human_vs_rhodopsin_ext.tabular
-  - ../../test-data/blastp_human_vs_pdb_seg_no.xml
-  - ../../test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular
-  - ../../test-data/blastp_human_vs_pdb_seg_no_converted_std.tabular
-  - ../../test-data/blastp_rhodopsin_vs_four_human.tabular
-  - ../../test-data/blastp_sample.xml
-  - ../../test-data/blastp_sample_converted.tabular
-  - ../../test-data/blastx_rhodopsin_vs_four_human.tabular
-  - ../../test-data/blastx_rhodopsin_vs_four_human.xml
-  - ../../test-data/blastx_rhodopsin_vs_four_human_all.tabular
-  - ../../test-data/blastx_rhodopsin_vs_four_human_converted.tabular
-  - ../../test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular
-  - ../../test-data/blastx_rhodopsin_vs_four_human_ext.tabular
-  - ../../test-data/blastx_sample.xml
-  - ../../test-data/blastx_sample_converted.tabular
-  - ../../test-data/cd00003.smp
-  - ../../test-data/cd00003_and_cd00008.aux
-  - ../../test-data/cd00003_and_cd00008.freq
-  - ../../test-data/cd00003_and_cd00008.loo
-  - ../../test-data/cd00003_and_cd00008.phr
-  - ../../test-data/cd00003_and_cd00008.pin
-  - ../../test-data/cd00003_and_cd00008.psd
-  - ../../test-data/cd00003_and_cd00008.psi
-  - ../../test-data/cd00003_and_cd00008.psq
-  - ../../test-data/cd00003_and_cd00008.rps
-  - ../../test-data/cd00008.smp
-  - ../../test-data/chimera.fasta
-  - ../../test-data/chimera.fasta.gz
-  - ../../test-data/convert2blastmask_four_human_masked.maskinfo-asn1
-  - ../../test-data/convert2blastmask_four_human_masked.maskinfo-asn1-binary
-  - ../../test-data/dustmasker_three_human.fasta
-  - ../../test-data/dustmasker_three_human.maskinfo-asn1
-  - ../../test-data/dustmasker_three_human.maskinfo-asn1-binary
-  - ../../test-data/empty_file.dat
-  - ../../test-data/four_human_proteins.dbinfo.txt
-  - ../../test-data/four_human_proteins.fasta
-  - ../../test-data/four_human_proteins.fasta.log.txt
-  - ../../test-data/four_human_proteins.fasta.phd
-  - ../../test-data/four_human_proteins.fasta.phi
-  - ../../test-data/four_human_proteins.fasta.phr
-  - ../../test-data/four_human_proteins.fasta.pin
-  - ../../test-data/four_human_proteins.fasta.pog
-  - ../../test-data/four_human_proteins.fasta.psd
-  - ../../test-data/four_human_proteins.fasta.psi
-  - ../../test-data/four_human_proteins.fasta.psq
-  - ../../test-data/four_human_proteins_masked.fasta
-  - ../../test-data/four_human_proteins_taxid.fasta.log.txt
-  - ../../test-data/four_human_proteins_taxid.fasta.phd
-  - ../../test-data/four_human_proteins_taxid.fasta.phi
-  - ../../test-data/four_human_proteins_taxid.fasta.phr
-  - ../../test-data/four_human_proteins_taxid.fasta.pin
-  - ../../test-data/four_human_proteins_taxid.fasta.pog
-  - ../../test-data/four_human_proteins_taxid.fasta.psd
-  - ../../test-data/four_human_proteins_taxid.fasta.psi
-  - ../../test-data/four_human_proteins_taxid.fasta.psq
-  - ../../test-data/rhodopsin_nucs.dbinfo.txt
-  - ../../test-data/rhodopsin_nucs.fasta
-  - ../../test-data/rhodopsin_nucs.fasta.gz
-  - ../../test-data/rhodopsin_nucs.fasta.log.txt
-  - ../../test-data/rhodopsin_nucs.fasta.nhd
-  - ../../test-data/rhodopsin_nucs.fasta.nhi
-  - ../../test-data/rhodopsin_nucs.fasta.nhr
-  - ../../test-data/rhodopsin_nucs.fasta.nin
-  - ../../test-data/rhodopsin_nucs.fasta.nog
-  - ../../test-data/rhodopsin_nucs.fasta.nsd
-  - ../../test-data/rhodopsin_nucs.fasta.nsi
-  - ../../test-data/rhodopsin_nucs.fasta.nsq
-  - ../../test-data/rhodopsin_nucs.fasta.nnd
-  - ../../test-data/rhodopsin_nucs.fasta.nni
-  - ../../test-data/rhodopsin_nucs.no_gi.fasta
-  - ../../test-data/rhodopsin_nucs.blastdbcmd.txt
-  - ../../test-data/rhodopsin_bufo.fasta
-  - ../../test-data/rhodopsin_proteins.fasta
-  - ../../test-data/segmasker_four_human.fasta
-  - ../../test-data/segmasker_four_human.maskinfo-asn1
-  - ../../test-data/segmasker_four_human.maskinfo-asn1-binary
-  - ../../test-data/tblastn_four_human_vs_rhodopsin.html
-  - ../../test-data/tblastn_four_human_vs_rhodopsin.tabular
-  - ../../test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular
-  - ../../test-data/tblastn_four_human_vs_rhodopsin.xml
-  - ../../test-data/tblastn_four_human_vs_rhodopsin_ext.tabular
-  - ../../test-data/tblastx_rhodopsin_vs_three_human.tabular
-  - ../../test-data/three_human_mRNA.dbinfo.txt
-  - ../../test-data/three_human_mRNA.fasta
-  - ../../test-data/three_human_mRNA.fasta.gz
-  - ../../test-data/three_human_mRNA.fasta.log.txt
-  - ../../test-data/three_human_mRNA.fasta.nhd
-  - ../../test-data/three_human_mRNA.fasta.nhi
-  - ../../test-data/three_human_mRNA.fasta.nhr
-  - ../../test-data/three_human_mRNA.fasta.nin
-  - ../../test-data/three_human_mRNA.fasta.nog
-  - ../../test-data/three_human_mRNA.fasta.nsd
-  - ../../test-data/three_human_mRNA.fasta.nsi
-  - ../../test-data/three_human_mRNA.fasta.nsq
-  - ../../test-data/tool_data_table_conf.xml.test
+  - test-data/blastdb.loc
+  - test-data/blastdb_d.loc
+  - test-data/blastdb_p.loc
+  - test-data/blastn_arabidopsis.extended.tabular
+  - test-data/blastn_arabidopsis.standard.tabular
+  - test-data/blastn_arabidopsis.xml
+  - test-data/blastn_chimera_vs_three_human_max1.tabular
+  - test-data/blastn_chimera_vs_three_human_max1.txt
+  - test-data/blastn_rhodopsin_vs_three_human.columns.tabular
+  - test-data/blastn_rhodopsin_vs_three_human.tabular
+  - test-data/blastn_rhodopsin_vs_three_human.xml
+  - test-data/blastn_rhodopsin_vs_three_human_converted.tabular
+  - test-data/blastn_chimera_vs_three_human_db.tabular
+  - test-data/blastn_chimera_vs_rhodopsin_db.tabular
+  - test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular
+  - test-data/blastp_four_human_vs_rhodopsin.tabular
+  - test-data/blastp_four_human_vs_rhodopsin.xml
+  - test-data/blastp_four_human_vs_rhodopsin_converted.tabular
+  - test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular
+  - test-data/blastp_four_human_vs_rhodopsin_ext.tabular
+  - test-data/blastp_human_vs_pdb_seg_no.xml
+  - test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular
+  - test-data/blastp_human_vs_pdb_seg_no_converted_std.tabular
+  - test-data/blastp_rhodopsin_vs_four_human.tabular
+  - test-data/blastp_sample.xml
+  - test-data/blastp_sample_converted.tabular
+  - test-data/blastx_rhodopsin_vs_four_human.tabular
+  - test-data/blastx_rhodopsin_vs_four_human.xml
+  - test-data/blastx_rhodopsin_vs_four_human_all.tabular
+  - test-data/blastx_rhodopsin_vs_four_human_converted.tabular
+  - test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular
+  - test-data/blastx_rhodopsin_vs_four_human_ext.tabular
+  - test-data/blastx_sample.xml
+  - test-data/blastx_sample_converted.tabular
+  - test-data/cd00003.smp
+  - test-data/cd00003_and_cd00008.aux
+  - test-data/cd00003_and_cd00008.freq
+  - test-data/cd00003_and_cd00008.loo
+  - test-data/cd00003_and_cd00008.phr
+  - test-data/cd00003_and_cd00008.pin
+  - test-data/cd00003_and_cd00008.psd
+  - test-data/cd00003_and_cd00008.psi
+  - test-data/cd00003_and_cd00008.psq
+  - test-data/cd00003_and_cd00008.rps
+  - test-data/cd00008.smp
+  - test-data/chimera.fasta
+  - test-data/chimera.fasta.gz
+  - test-data/convert2blastmask_four_human_masked.maskinfo-asn1
+  - test-data/convert2blastmask_four_human_masked.maskinfo-asn1-binary
+  - test-data/dustmasker_three_human.fasta
+  - test-data/dustmasker_three_human.maskinfo-asn1
+  - test-data/dustmasker_three_human.maskinfo-asn1-binary
+  - test-data/empty_file.dat
+  - test-data/four_human_proteins.dbinfo.txt
+  - test-data/four_human_proteins.fasta
+  - test-data/four_human_proteins.fasta.log.txt
+  - test-data/four_human_proteins.fasta.phd
+  - test-data/four_human_proteins.fasta.phi
+  - test-data/four_human_proteins.fasta.phr
+  - test-data/four_human_proteins.fasta.pin
+  - test-data/four_human_proteins.fasta.pog
+  - test-data/four_human_proteins.fasta.psd
+  - test-data/four_human_proteins.fasta.psi
+  - test-data/four_human_proteins.fasta.psq
+  - test-data/four_human_proteins_masked.fasta
+  - test-data/four_human_proteins_taxid.fasta.log.txt
+  - test-data/four_human_proteins_taxid.fasta.phd
+  - test-data/four_human_proteins_taxid.fasta.phi
+  - test-data/four_human_proteins_taxid.fasta.phr
+  - test-data/four_human_proteins_taxid.fasta.pin
+  - test-data/four_human_proteins_taxid.fasta.pog
+  - test-data/four_human_proteins_taxid.fasta.psd
+  - test-data/four_human_proteins_taxid.fasta.psi
+  - test-data/four_human_proteins_taxid.fasta.psq
+  - test-data/rhodopsin_nucs.dbinfo.txt
+  - test-data/rhodopsin_nucs.fasta
+  - test-data/rhodopsin_nucs.fasta.gz
+  - test-data/rhodopsin_nucs.fasta.log.txt
+  - test-data/rhodopsin_nucs.fasta.nhd
+  - test-data/rhodopsin_nucs.fasta.nhi
+  - test-data/rhodopsin_nucs.fasta.nhr
+  - test-data/rhodopsin_nucs.fasta.nin
+  - test-data/rhodopsin_nucs.fasta.nog
+  - test-data/rhodopsin_nucs.fasta.nsd
+  - test-data/rhodopsin_nucs.fasta.nsi
+  - test-data/rhodopsin_nucs.fasta.nsq
+  - test-data/rhodopsin_nucs.fasta.nnd
+  - test-data/rhodopsin_nucs.fasta.nni
+  - test-data/rhodopsin_nucs.no_gi.fasta
+  - test-data/rhodopsin_nucs.blastdbcmd.txt
+  - test-data/rhodopsin_bufo.fasta
+  - test-data/rhodopsin_proteins.fasta
+  - test-data/segmasker_four_human.fasta
+  - test-data/segmasker_four_human.maskinfo-asn1
+  - test-data/segmasker_four_human.maskinfo-asn1-binary
+  - test-data/tblastn_four_human_vs_rhodopsin.html
+  - test-data/tblastn_four_human_vs_rhodopsin.tabular
+  - test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular
+  - test-data/tblastn_four_human_vs_rhodopsin.xml
+  - test-data/tblastn_four_human_vs_rhodopsin_ext.tabular
+  - test-data/tblastx_rhodopsin_vs_three_human.tabular
+  - test-data/three_human_mRNA.dbinfo.txt
+  - test-data/three_human_mRNA.fasta
+  - test-data/three_human_mRNA.fasta.gz
+  - test-data/three_human_mRNA.fasta.log.txt
+  - test-data/three_human_mRNA.fasta.nhd
+  - test-data/three_human_mRNA.fasta.nhi
+  - test-data/three_human_mRNA.fasta.nhr
+  - test-data/three_human_mRNA.fasta.nin
+  - test-data/three_human_mRNA.fasta.nog
+  - test-data/three_human_mRNA.fasta.nsd
+  - test-data/three_human_mRNA.fasta.nsi
+  - test-data/three_human_mRNA.fasta.nsq
+  - test-data/tool_data_table_conf.xml.test
   - ../../tool-data/blastdb.loc.sample
   - ../../tool-data/blastdb_d.loc.sample
   - ../../tool-data/blastdb_p.loc.sample