Mercurial > repos > devteam > ncbi_blast_plus
diff tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @ 9:9dabbfd73c8a draft
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
Also includes other minor improvements.
author | peterjc |
---|---|
date | Thu, 25 Apr 2013 09:38:37 -0400 |
parents | 1f546099212f |
children | 70e7dcbf6573 |
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--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Feb 19 12:49:43 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 @@ -1,7 +1,11 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.17"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.19"> <description>Search translated nucleotide database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> + <requirements> + <requirement type="binary">tblastn</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> + </requirements> <version_command>tblastn -version</version_command> <command> ## The command is a Cheetah template which allows some Python based syntax. @@ -16,7 +20,7 @@ -subject "$db_opts.subject" #end if -evalue $evalue_cutoff --out $output1 +-out "$output1" ##Set the extended list here so if/when we add things, saved workflows are not affected #if str($out_format)=="ext": -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" @@ -48,13 +52,13 @@ <exit_code range=":-1" /> <!-- In case the return code has not been set propery check stderr too --> <regex match="Error:" /> - <regex match="EXception:" /> + <regex match="Exception:" /> </stdio> <inputs> <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> <conditional name="db_opts"> <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">BLAST Database</option> + <option value="db" selected="True">Locally installed BLAST database</option> <option value="histdb">BLAST database from your history</option> <option value="file">FASTA file from your history (see warning note below)</option> </param> @@ -154,7 +158,7 @@ </conditional> </inputs> <outputs> - <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"> + <data name="output1" format="tabular" label="tblastn on ${on_string}"> <change_format> <when input="out_format" value="0" format="txt"/> <when input="out_format" value="0 -html" format="html"/> @@ -166,9 +170,6 @@ </change_format> </data> </outputs> - <requirements> - <requirement type="binary">tblastn</requirement> - </requirements> <tests> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" />