| Previous changeset 49:17f84d08f5a6 (2020-09-08) Next changeset 51:1ebae91eb6e9 (2020-09-09) |
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Commit message:
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 71a7deb3a02f28262488e41c781fa918d1d14488-dirty" |
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modified:
test-data/four_human_proteins.dbinfo.txt test-data/rhodopsin_nucs.dbinfo.txt test-data/three_human_mRNA.dbinfo.txt tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml |
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| diff -r 17f84d08f5a6 -r 8146c9884047 test-data/four_human_proteins.dbinfo.txt --- a/test-data/four_human_proteins.dbinfo.txt Tue Sep 08 20:58:48 2020 +0000 +++ b/test-data/four_human_proteins.dbinfo.txt Wed Sep 09 13:12:55 2020 +0000 |
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| @@ -1,7 +1,3 @@ Database: Just 4 human proteins 4 sequences; 3,297 total residues -Date: Oct 31, 2017 4:23 PM Longest sequence: 1,382 residues - -Volumes: - /mnt/galaxy/repositories/galaxy_blast/test-data/four_human_proteins_taxid.fasta |
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| diff -r 17f84d08f5a6 -r 8146c9884047 test-data/rhodopsin_nucs.dbinfo.txt --- a/test-data/rhodopsin_nucs.dbinfo.txt Tue Sep 08 20:58:48 2020 +0000 +++ b/test-data/rhodopsin_nucs.dbinfo.txt Wed Sep 09 13:12:55 2020 +0000 |
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| @@ -1,7 +1,3 @@ Database: Rhodopsin nucleotides 6 sequences; 10,296 total bases -Date: Oct 31, 2017 4:23 PM Longest sequence: 4,301 bases - -Volumes: - /mnt/galaxy/repositories/galaxy_blast/test-data/rhodopsin_nucs.fasta |
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| diff -r 17f84d08f5a6 -r 8146c9884047 test-data/three_human_mRNA.dbinfo.txt --- a/test-data/three_human_mRNA.dbinfo.txt Tue Sep 08 20:58:48 2020 +0000 +++ b/test-data/three_human_mRNA.dbinfo.txt Wed Sep 09 13:12:55 2020 +0000 |
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| @@ -1,7 +1,3 @@ Database: Just 3 human mRNA sequences 3 sequences; 10,732 total bases -Date: Oct 31, 2017 4:23 PM Longest sequence: 4,796 bases - -Volumes: - /mnt/galaxy/repositories/galaxy_blast/test-data/three_human_mRNA.fasta |
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| diff -r 17f84d08f5a6 -r 8146c9884047 tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Tue Sep 08 20:58:48 2020 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Sep 09 13:12:55 2020 +0000 |
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| @@ -6,7 +6,7 @@ </macros> <expand macro="preamble" /> <command detect_errors="aggressive"> -blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" +blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path.replace(',',' ')}" -info -out "$info" </command> <inputs> <expand macro="input_conditional_choose_db_type" /> @@ -18,17 +18,22 @@ <test> <param name="db_opts|db_type" value="prot" /> <param name="db_opts|database" value="four_human_proteins" /> - <output name="info" file="four_human_proteins.dbinfo.txt" ftype="txt" lines_diff="4" /> + <output name="info" file="four_human_proteins.dbinfo.txt" ftype="txt" compare="contains" /> </test> <test> <param name="db_opts|db_type" value="nucl" /> <param name="db_opts|database" value="three_human_mRNA" /> - <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" lines_diff="4" /> + <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" compare="contains" /> </test> <test> <param name="db_opts|db_type" value="nucl" /> <param name="db_opts|database" value="rhodopsin_nucs" /> - <output name="info" file="rhodopsin_nucs.dbinfo.txt" ftype="txt" lines_diff="4" /> + <output name="info" file="rhodopsin_nucs.dbinfo.txt" ftype="txt" compare="contains" /> + </test> + <test> + <param name="db_opts|db_type" value="nucl" /> + <param name="db_opts|database" value="three_human_mRNA,rhodopsin_nucs" /> + <output name="info" file="three_human_mRNA_and_rhodopsin_nucs.dbinfo.txt" ftype="txt" compare="contains" /> </test> </tests> <help> |
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| diff -r 17f84d08f5a6 -r 8146c9884047 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Tue Sep 08 20:58:48 2020 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Sep 09 13:12:55 2020 +0000 |
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| @@ -106,7 +106,8 @@ </test> <test> <param name="db_opts|db_type" value="nucl" /> - <param name="db_opts|database" value="rhodopsin_nucs" /> + <!-- look in two databases for this entry --> + <param name="db_opts|database" value="rhodopsin_nucs,three_human_mRNA" /> <param name="id_opts|id_type" value="prompt" /> <param name="id_opts|entries" value="gi|2734705|gb|U59921.1|BBU59921" /> <param name="outfmt" value="original" /> |