comparison tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 4:9d5beacae92b draft

Uploaded v0.0.13 which uses the recently added error handling. No longer bundles the hide_stderr.py script which is now redundant.

3:643338ac83c0

<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.12">
    <description>Search nucleotide database with nucleotide 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" merge_outputs="output1"></parallelism>
    <version_command>blastn -version</version_command>
    <command interpreter="python">hide_stderr.py
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
blastn
-query "$query"
#if $db_opts.db_opts_selector == "db":

$adv_opts.ungapped
$adv_opts.parse_deflines
## End of advanced options:
#end if
    </command>
    <inputs>
        <param name="query" type="data" format="fasta" label="Nucleotide 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>

4:9d5beacae92b

<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.13">
    <description>Search nucleotide database with nucleotide 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" merge_outputs="output1"></parallelism>
    <version_command>blastn -version</version_command>
    <command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
blastn
-query "$query"
#if $db_opts.db_opts_selector == "db":

$adv_opts.ungapped
$adv_opts.parse_deflines
## End of advanced options:
#end if
    </command>
    <stdio>
        <exit_code range="1:" />
	<exit_code range="://0" />
    </stdio>
    <inputs>
        <param name="query" type="data" format="fasta" label="Nucleotide 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>