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changeset 50:8146c9884047 draft

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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 71a7deb3a02f28262488e41c781fa918d1d14488-dirty"
author peterjc
date Wed, 09 Sep 2020 13:12:55 +0000
parents 17f84d08f5a6
children 1ebae91eb6e9
files 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
diffstat 5 files changed, 11 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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>
--- 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
@@ -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" />