comparison macros.xml @ 5:bde9421d7918 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea

4:a69e00e985da

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.2.5">python-chado</requirement>
            <requirement type="package" version="1.5">jq</requirement>
            <yield/>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>
            <regex level="fatal" match="Exception:" source="stderr" />
            <regex level="fatal" match="error" source="stderr" />
            <exit_code range="1:" />
        </stdio>
    </xml>

    <token name="@WRAPPER_VERSION@">2.2.5</token>

    <xml name="citation">
        <citations>
        </citations>
    </xml>

        Python-cado provides several tools allowing to load data into a remote Chado database.
    ]]></token>

    <token name="@HELP@"><![CDATA[
    ]]></token>

    <token name="@AUTH@"><![CDATA[
        echo "__default: local" > '.auth.yml' &&
        echo "local:" >> '.auth.yml' &&
        echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
        echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
        echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
        echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
        echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
        echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&

        CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
    ]]></token>

    <xml name="sanitized">
        <sanitizer>
            <valid initial="string.printable">

               argument="--rel-subject-type"
               type="text"
               label="Sequence type of the parent"
               help="this should be a Sequence Ontology term" />
    </xml>
</macros>

5:bde9421d7918

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.2.6">python-chado</requirement>
            <requirement type="package" version="1.5">jq</requirement>
            <requirement type="package" version="@PG_VERSION@">postgresql</requirement>
            <requirement type="package" version="0.1">pglite</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@PG_VERSION@">11.2</token>

    <xml name="stdio">
        <stdio>
            <regex level="fatal" match="Exception:" source="stderr" />
            <regex level="fatal" match="error" source="stderr" />
            <exit_code range="1:" />
        </stdio>
    </xml>

    <token name="@WRAPPER_VERSION@">2.2.6</token>

    <xml name="citation">
        <citations>
        </citations>
    </xml>

        Python-cado provides several tools allowing to load data into a remote Chado database.
    ]]></token>

    <token name="@HELP@"><![CDATA[
    ]]></token>

    <xml name="sanitized">
        <sanitizer>
            <valid initial="string.printable">

               argument="--rel-subject-type"
               type="text"
               label="Sequence type of the parent"
               help="this should be a Sequence Ontology term" />
    </xml>

    <xml name="psql_target">
      <conditional name="psql_target">
         <param name="method" type="select" label="Chado Database" help="If you select 'Remote database' make sure credentials are defined in environment variables">
              <option value="remote">Remote database</option>
              <option value="pgtools">Database from history</option>
          </param>
          <when value="remote"/>
          <when value="pgtools">
            <param name="infile" type="data" format="postgresql" label="Input database" />
            <param name="schema" type="text" label="Schema containing Chado tables" value="public" help="Can be 'chado' for a Tripal database"/>
          </when>
      </conditional>
    </xml>

    <token name="@AUTH@"><![CDATA[
        if [ -z "$CHAKIN_GLOBAL_CONFIG_PATH" ]; then
          echo "__default: local" > '.auth.yml' &&
          echo "local:" >> '.auth.yml' &&
          echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
          echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
          echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
          echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
          echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
          echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&

          export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
        ; fi
    ]]></token>

    <token name="@START_PSQL@"><![CDATA[
        #if $psql_target.method == 'pgtools'
            tar -xjvf '$psql_target.infile' > /dev/null &&
            . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema'
        #else
            @AUTH@
        #end if
    ]]></token>

    <token name="@STOP_PSQL@"><![CDATA[
        #if $psql_target.method == 'pgtools'
            pglite stop -d ./postgresql &&
            timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done'
            ;
            ## Make sure psql is stopped even if loading script failed
            pglite stop -d ./postgresql || true
        #end if
    ]]></token>

    <token name="@ZIP_PSQL@"><![CDATA[
        #if $psql_target.method == 'pgtools'
            pglite stop -d ./postgresql &&
            timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' &&
            tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null
            ;
            ## Make sure psql is stopped even if loading script failed
            pglite stop -d ./postgresql || true
        #end if
    ]]></token>
</macros>