Mercurial > repos > devteam > ncbi_blast_plus
changeset 2:6119ddccd8a3 draft
Uploaded v0.1.02 preview 3, disable tests using blastdb*.loc since not supported on the ToolShed (yet).
| author | peterjc |
|---|---|
| date | Thu, 02 Apr 2015 04:48:24 -0400 |
| parents | 5e9d5e536b79 |
| children | e98f6bd363ba |
| files | 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_macros.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml |
| diffstat | 6 files changed, 19 insertions(+), 4 deletions(-) [+] |
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--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Tue Mar 03 05:32:18 2015 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Thu Apr 02 04:48:24 2015 -0400 @@ -16,6 +16,8 @@ <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> </outputs> <tests> + <!-- Disable for ToolShed where *.loc tests not yet supported + See https://github.com/peterjc/galaxy_blast/issues/53 <test> <param name="db_opts|db_type" value="prot" /> <param name="db_opts|database" value="four_human_proteins" /> @@ -26,6 +28,7 @@ <param name="db_opts|database" value="three_human_mRNA" /> <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" lines_diff="4" /> </test> + --> </tests> <help>
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Tue Mar 03 05:32:18 2015 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Thu Apr 02 04:48:24 2015 -0400 @@ -71,6 +71,8 @@ <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" /> </outputs> <tests> + <!-- Disable for ToolShed where *.loc tests not yet supported + See https://github.com/peterjc/galaxy_blast/issues/53 <test> <param name="db_opts|db_type" value="prot" /> <param name="db_opts|database" value="four_human_proteins" /> @@ -79,6 +81,7 @@ <param name="outfmt" value="original" /> <output name="seq" file="four_human_proteins.fasta" ftype="fasta" /> </test> + --> </tests> <help>
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Mar 03 05:32:18 2015 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Apr 02 04:48:24 2015 -0400 @@ -108,6 +108,8 @@ <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> </test> + <!-- Disable for ToolShed where *.loc tests not yet supported + See https://github.com/peterjc/galaxy_blast/issues/53 <test> <param name="query" value="chimera.fasta" ftype="fasta" /> <param name="db_opts_selector" value="db" /> @@ -126,6 +128,7 @@ <param name="max_hits" value="1" /> <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" /> </test> + --> </tests> <help>
--- a/tools/ncbi_blast_plus/ncbi_macros.xml Tue Mar 03 05:32:18 2015 -0500 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Thu Apr 02 04:48:24 2015 -0400 @@ -66,7 +66,7 @@ <option value="slen">slen = Subject sequence length</option> <option value="salltitles">salltitles = All subject title(s), separated by a '<>'</option> </param> - <param name="ids_cols" type="select" multiple="true" display="checkboxes" label="Other identifer columns"> + <param name="ids_cols" type="select" multiple="true" display="checkboxes" label="Other identifier columns"> <option value="qgi">qgi = Query GI</option> <option value="qacc">qacc = Query accesion</option> <option value="qaccver">qaccver = Query accesion.version</option> @@ -313,9 +313,9 @@ label="Restrict search of database to a given set of ID's" help="This feature provides a means to exclude ID's from a BLAST database search. The expectation values in the BLAST results are based upon the sequences actually searched, and not on the underlying database. Note this cannot be used when comparing against a FASTA file."> <option value="none" selected="True">No restriction, search the entire database</option> - <option value="gilist">GI identifers</option> - <option value="negative_gilist">Negative GI identifers</option> - <option value="seqidlist">Sequence identifers (SeqId's)</option> + <option value="gilist">GI identifiers</option> + <option value="negative_gilist">Negative GI identifiers</option> + <option value="seqidlist">Sequence identifiers (SeqId's)</option> </param> <when value="none" /> <when value="gilist">
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Tue Mar 03 05:32:18 2015 -0500 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu Apr 02 04:48:24 2015 -0400 @@ -55,6 +55,8 @@ </data> </outputs> <tests> + <!-- Disable for ToolShed where *.loc tests not yet supported + See https://github.com/peterjc/galaxy_blast/issues/53 <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="db" /> @@ -63,6 +65,7 @@ <param name="out_format" value="6" /> <output name="output1" file="empty_file.dat" ftype="tabular" /> </test> + --> </tests> <help>
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Tue Mar 03 05:32:18 2015 -0500 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu Apr 02 04:48:24 2015 -0400 @@ -53,6 +53,8 @@ </data> </outputs> <tests> + <!-- Disable for ToolShed where *.loc tests not yet supported + See https://github.com/peterjc/galaxy_blast/issues/53 <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> <param name="db_opts_selector" value="db" /> @@ -61,6 +63,7 @@ <param name="out_format" value="6" /> <output name="output1" file="empty_file.dat" ftype="tabular" /> </test> + --> </tests> <help>