comparison tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml @ 15:c16c30e9ad5b draft

Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)

14:2fe07f50a41e

<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.01">
    <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo -->
    <description>masks low complexity regions</description>
    <macros>
        <token name="@BINARY@">dustmasker</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <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
dustmasker
#if $db_opts.db_opts_selector == "db":
  -in "${db_opts.database.fields.path}" -infmt blastdb
#elif $db_opts.db_opts_selector == "histdb":
  -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb
#else:
  -in "$subject" -infmt fasta
#end if
-out "$outfile"
-window $window -level $level -linker $linker -outfmt $outformat
    </command>
    <expand macro="stdio" />
    <inputs>
        <expand macro="input_conditional_nucleotide_db" />
        <param name="window" type="integer" value="64" label="DUST window length" />
        <param name="level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" />
        <param name="linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" />

.. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549

**References**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers (a more specific paper covering this wrapper is planned):

@REFERENCES@
    </help>
    <expand macro="blast_citations" />
</tool>

15:c16c30e9ad5b

<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.03">
    <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo -->
    <description>masks low complexity regions</description>
    <macros>
        <token name="@BINARY@">dustmasker</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="preamble" />
    <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
dustmasker
#if $db_opts.db_opts_selector == "db":
  -in "${db_opts.database.fields.path}" -infmt blastdb
#elif $db_opts.db_opts_selector == "histdb":
  -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb
#else:
  -in "$subject" -infmt fasta
#end if
-out "$outfile"
-window $window -level $level -linker $linker -outfmt $outformat
    </command>
    <inputs>
        <expand macro="input_conditional_nucleotide_db" />
        <param name="window" type="integer" value="64" label="DUST window length" />
        <param name="level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" />
        <param name="linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" />

.. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549

**References**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

@REFERENCES@
    </help>
    <expand macro="blast_citations" />
</tool>