comparison tools/ncbi_blast_plus/ncbi_macros.xml @ 27:6f8ea4b9a2c4 draft

"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"

26:2889433c7ae1

<macros>
    <token name="@WRAPPER_VERSION@">0.3.3</token>
    <xml name="parallelism">
        <!-- 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" merge_outputs="output1" />
    </xml>

    <xml name="preamble">
        <requirements>
            <requirement type="package" version="2.7.1">blast</requirement>
        </requirements>
        <version_command>@BINARY@ -version</version_command>
    </xml>

    <xml name="nucl_query">

            <param argument="-db_type" type="select" label="Type of BLAST database">
              <option value="nucl" selected="true">Nucleotide</option>
              <option value="prot">Protein</option>
            </param>
            <when value="nucl">
                <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database">
                    <options from_data_table="blastdb" />
                </param>
            </when>
            <when value="prot">
                <param name="database" argument="-db" type="select" multiple="true" label="Protein BLAST database">
                    <options from_data_table="blastdb_p" />
                </param>
            </when>
        </conditional>
    </xml>

    <xml name="input_parse_deflines">

#else:
  -query '${query}'
#end if
    ]]></token>

    <token name="@BLAST_DB_SUBJECT@"><![CDATA[
#if $db_opts.db_opts_selector == "db":
  -db '${" ".join(str($db_opts.database.fields.path).split(","))}'
#elif $db_opts.db_opts_selector == "histdb":
  -db '${os.path.join($db_opts.histdb.extra_files_path, "blastdb")}'

#else
'${db_opts.subject.name}'
#end if
]]></token>

    <token name="@REFERENCES@"><![CDATA[
Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015).
NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39
https://doi.org/10.1186/s13742-015-0080-7

27:6f8ea4b9a2c4

<macros>
    <token name="@TOOL_VERSION@">2.7.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">16.10</token>
    <xml name="parallelism">
        <!-- 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" merge_outputs="output1" />
    </xml>

    <xml name="preamble">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">blast</requirement>
        </requirements>
        <version_command>@BINARY@ -version</version_command>
    </xml>

    <xml name="nucl_query">

            <param argument="-db_type" type="select" label="Type of BLAST database">
              <option value="nucl" selected="true">Nucleotide</option>
              <option value="prot">Protein</option>
            </param>
            <when value="nucl">
                <conditional name="db_origin">
                    <param name="db_origin_selector" type="select" label="Subject database/sequences">
                          <option value="db" selected="true">Locally installed BLAST database</option>
                          <option value="histdb">BLAST database from your history</option>
                    </param>
                    <when value="db">
                        <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database">
                            <options from_data_table="blastdb" />
                        </param>
                        <param name="histdb" type="hidden" value="" />
                    </when>
                    <when value="histdb">
                        <param name="database" type="hidden" value="" />
                        <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" />
                    </when>
                </conditional>
            </when>
            <when value="prot">
                <conditional name="db_origin">
                    <param name="db_origin_selector" type="select" label="Subject database/sequences">
                          <option value="db" selected="true">Locally installed BLAST database</option>
                          <option value="histdb">BLAST database from your history</option>
                      </param>
                      <when value="db">
                          <param name="database" argument="-db" type="select" multiple="true" label="Protein BLAST database">
                            <options from_data_table="blastdb_p" />
                        </param>
                        <param name="histdb" type="hidden" value="" />
                      </when>
                      <when value="histdb">
                        <param name="database" type="hidden" value="" />
                        <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" />
                      </when>
                </conditional>
            </when>
        </conditional>
    </xml>

    <xml name="input_parse_deflines">

#else:
  -query '${query}'
#end if
    ]]></token>

    <!-- Implement -dbtype and -db command line options (in blastdbcmd) -->
    <token name="@DBCMD_OPTS@"><![CDATA[
-dbtype "$db_opts.db_type"
#if $db_opts.db_origin.db_origin_selector=="db":
  -db "${db_opts.db_origin.database.fields.path.replace(',',' ')}"
#else if $db_opts.db_origin.db_origin_selector=="histdb":
  -db '${os.path.join($db_opts.db_origin.histdb.extra_files_path, "blastdb")}'
#end if
    ]]></token>

    <!-- Implement -db ... / -subject ... command line options -->
    <token name="@BLAST_DB_SUBJECT@"><![CDATA[
#if $db_opts.db_opts_selector == "db":
  -db '${" ".join(str($db_opts.database.fields.path).split(","))}'
#elif $db_opts.db_opts_selector == "histdb":
  -db '${os.path.join($db_opts.histdb.extra_files_path, "blastdb")}'

#else
'${db_opts.subject.name}'
#end if
]]></token>

    <!-- @ON_DBCMD_OPTS@ is for use with @DBCMD_OPTS@ -->
    <token name="@ON_DBCMD_OPTS@"><![CDATA[
#if str($db_opts.db_origin.db_origin_selector)=="db"
'${db_opts.db_origin.database}'
#else
'${db_opts.db_origin.histdb.name}'
#end if
]]></token>

    <token name="@REFERENCES@"><![CDATA[
Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015).
NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39
https://doi.org/10.1186/s13742-015-0080-7