comparison tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @ 6:a23b0627623c draft

Uploaded v0.0.15, clearer warning about searching against a FASTA file.

5:393a7a35383c

<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.14">
    <description>Search protein database with translated 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,histdb" merge_outputs="output1"></parallelism>
    <version_command>blastx -version</version_command>
    <command>

        <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>
              <option value="histdb">BLAST database from your history</option>
              <option value="file">FASTA file from your history (pairwise e-values)</option>
            </param>
            <when value="db">
                <param name="database" type="select" label="Protein BLAST database">
                    <options from_file="blastdb_p.loc">
                      <column name="value" index="0"/>

**What it does**

Search a *protein database* using a *translated nucleotide query*,
using the NCBI BLAST+ blastx command line tool.

-----

**Output format**

Because Galaxy focuses on processing tabular data, the default output of this

6:a23b0627623c

<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.15">
    <description>Search protein database with translated 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,histdb" merge_outputs="output1"></parallelism>
    <version_command>blastx -version</version_command>
    <command>

        <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>
              <option value="histdb">BLAST database from your history</option>
              <option value="file">FASTA file from your history (see warning note below)</option>
            </param>
            <when value="db">
                <param name="database" type="select" label="Protein BLAST database">
                    <options from_file="blastdb_p.loc">
                      <column name="value" index="0"/>

**What it does**

Search a *protein database* using a *translated nucleotide query*,
using the NCBI BLAST+ blastx command line tool.

.. class:: warningmark

You can also search against a FASTA file of subject protein
sequences. This is *not* advised because it is slower (only one
CPU is used), but more importantly gives e-values for pairwise
searches (very small e-values which will look overly signficiant).
In most cases you should instead turn the other FASTA file into a
database first using *makeblastdb* and search against that.

-----

**Output format**

Because Galaxy focuses on processing tabular data, the default output of this