Manifests can point at local test-data folders now

README.rst

@@ -136,11 +136,10 @@ datatype definitions (obsolete), and ``data_managers`` contains Galaxy Data
 Managers for tasks like setting up local copies of NCBI BLAST databases
 (currently unfinished).
 
-All of these child folders contain additional README files, which cover
-things like how to install each tool manually or via the Galaxy Tool Shed.
-
-Additionally there is a shared ``test-data`` folder used for functional test
-sample data, and a shared ``tool-data`` folder used for configuration files.
+All of these child folders contain additional README files, which cover things
+like how to install each tool manually or via the Galaxy Tool Shed, subfolder
+``test-data`` for functional test sample data, and sometimes a subfolder
+``tool-data`` for configuration files.
 
 
 Installation

tools/blast2go/.shed.yml

@@ -20,12 +20,12 @@ categories:
 - Sequence Analysis
 type: unrestricted
 include:
-- strip_components: 2
+- strip_components: 0
   source:
-  - ../../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
+  - test-data/blastp_sample.blast2go.tabular
+  - test-data/blastp_sample.xml
+  - tool-data/blast2go.loc.sample
+  - README.rst
+  - blast2go.py
+  - blast2go.xml
+  - massage_xml_for_blast2go.py

tools/blast_rbh/.shed.yml

@@ -11,22 +11,22 @@ categories:
 - Sequence Analysis
 type: unrestricted
 include:
-- strip_components: 2
+- strip_components: 0
   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
-  - ../../tools/blast_rbh/README.rst
-  - ../../tools/blast_rbh/best_hits.py
-  - ../../tools/blast_rbh/blast_rbh.py
-  - ../../tools/blast_rbh/blast_rbh.xml
+  - 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
+  - README.rst
+  - best_hits.py
+  - blast_rbh.py
+  - blast_rbh.xml

tools/blastxml_to_top_descr/.shed.yml

@@ -25,12 +25,12 @@ categories:
 - Text Manipulation
 type: unrestricted
 include:
-- strip_components: 2
+- strip_components: 0
   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
-  - ../../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
+  - 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
+  - README.rst
+  - blastxml_to_top_descr.py
+  - blastxml_to_top_descr.xml

tools/make_nr/.shed.yml

@@ -13,15 +13,15 @@ categories:
 - Sequence Analysis
 type: unrestricted
 include:
-- strip_components: 2
+- strip_components: 0
   source:
-  - ../../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
+  - README.rst
+  - make_nr.py
+  - 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