No need for relative path to local files

This was sensible for consistency with the top-level
shared tool-data and test-data folders, but we're
phasing that out to follow IUC standard layout

tools/blast2go/.shed.yml

@@ -25,7 +25,7 @@ include:
   - 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/blast2go/blast2go.xml
-  - ../../tools/blast2go/massage_xml_for_blast2go.py
+  - README.rst
+  - blast2go.py
+  - blast2go.xml
+  - massage_xml_for_blast2go.py

tools/blast_rbh/.shed.yml

@@ -26,7 +26,7 @@ include:
   - 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/blast_rbh/blast_rbh.xml
+  - README.rst
+  - best_hits.py
+  - blast_rbh.py
+  - blast_rbh.xml

tools/blastxml_to_top_descr/.shed.yml

@@ -31,6 +31,6 @@ include:
   - 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
+  - README.rst
+  - blastxml_to_top_descr.py
+  - blastxml_to_top_descr.xml

tools/make_nr/.shed.yml

@@ -15,9 +15,9 @@ type: unrestricted
 include:
 - strip_components: 2
   source:
-  - ../../tools/make_nr/README.rst
-  - ../../tools/make_nr/make_nr.py
-  - ../../tools/make_nr/make_nr.xml
+  - README.rst
+  - make_nr.py
+  - make_nr.xml
   - test-data/duplicates.fasta
   - test-data/duplicates.fasta.gz
   - test-data/duplicates.nr.fasta

tools/ncbi_blast_plus/.shed.yml

@@ -131,23 +131,23 @@ include:
   - ../../tool-data/blastdb_d.loc.sample
   - ../../tool-data/blastdb_p.loc.sample
   - ../../tool-data/tool_data_table_conf.xml.sample
-  - ../../tools/ncbi_blast_plus/get_species_taxids.xml
-  - ../../tools/ncbi_blast_plus/README.rst
-  - ../../tools/ncbi_blast_plus/blastxml_to_tabular.py
-  - ../../tools/ncbi_blast_plus/blastxml_to_tabular.xml
-  - ../../tools/ncbi_blast_plus/check_no_duplicates.py
-  - ../../tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml
-  - ../../tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
-  - ../../tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
-  - ../../tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
-  - ../../tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
-  - ../../tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml
-  - ../../tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml
-  - ../../tools/ncbi_blast_plus/ncbi_macros.xml
-  - ../../tools/ncbi_blast_plus/ncbi_makeblastdb.xml
-  - ../../tools/ncbi_blast_plus/ncbi_makeprofiledb.xml
-  - ../../tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml
-  - ../../tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
-  - ../../tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml
-  - ../../tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
-  - ../../tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+  - get_species_taxids.xml
+  - README.rst
+  - blastxml_to_tabular.py
+  - blastxml_to_tabular.xml
+  - check_no_duplicates.py
+  - ncbi_blastdbcmd_info.xml
+  - ncbi_blastdbcmd_wrapper.xml
+  - ncbi_blastn_wrapper.xml
+  - ncbi_blastp_wrapper.xml
+  - ncbi_blastx_wrapper.xml
+  - ncbi_convert2blastmask_wrapper.xml
+  - ncbi_dustmasker_wrapper.xml
+  - ncbi_macros.xml
+  - ncbi_makeblastdb.xml
+  - ncbi_makeprofiledb.xml
+  - ncbi_rpsblast_wrapper.xml
+  - ncbi_rpstblastn_wrapper.xml
+  - ncbi_segmasker_wrapper.xml
+  - ncbi_tblastn_wrapper.xml
+  - ncbi_tblastx_wrapper.xml