comparison macros.xml @ 10:154d806aad47 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit e579248f105865ce7f2f237ab6fb3f10aab4c582

9:1455d3e7f191

<macros>
    <import>msfragger_macros.xml</import>
    <token name="@TOOL_VERSION@">23.0</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@TOOL_PROFILE@">25.1</token>

    <!--
        These keys were generated ONLY for use by the Galaxy tool wrapper, and only after
        the user has selected agreed to the academic-use only terms in the tool wrapper.

      First genericizes unknown sequence headers in the database.
      Then adds decoys, or decoys and contaminants depending on user selection.
    -->
    <token name="@PREPARE_DATABASE@"><![CDATA[
        '$__tool_directory__/genericize_db.py' $database_name genericized_db.fas &&

        #if str($database_options) != 'none'
            philosopher workspace --init &&
            philosopher database --custom genericized_db.fas --prefix rev_
            #if str($database_options) == 'decoy_and_contam'

10:154d806aad47

<macros>
    <import>msfragger_macros.xml</import>
    <token name="@TOOL_VERSION@">23.0</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@TOOL_PROFILE@">25.1</token>

    <!--
        These keys were generated ONLY for use by the Galaxy tool wrapper, and only after
        the user has selected agreed to the academic-use only terms in the tool wrapper.

      First genericizes unknown sequence headers in the database.
      Then adds decoys, or decoys and contaminants depending on user selection.
    -->
    <token name="@PREPARE_DATABASE@"><![CDATA[
        python '$__tool_directory__/genericize_db.py' $database_name genericized_db.fas &&

        #if str($database_options) != 'none'
            philosopher workspace --init &&
            philosopher database --custom genericized_db.fas --prefix rev_
            #if str($database_options) == 'decoy_and_contam'