view macros.xml @ 0:51ac1ffb4f38 draft

planemo upload for repository commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
author gga
date Thu, 21 Jun 2018 08:44:11 -0400
children 8c5e06b4b387
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<?xml version="1.0"?>
    <xml name="requirements">
            <requirement type="package" version="2.1.2">python-chado</requirement>

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

    <token name="@WRAPPER_VERSION@">2.1.1</token>

    <xml name="citation">

    <token name="@HELP_OVERVIEW@"><![CDATA[
        **Python-chado Overview**

        Python-cado provides several tools allowing to load data into a remote Chado database.

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

    <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' &&


    <xml name="sanitized">
            <valid initial="string.printable">
                <remove value="&apos;"/>
            <mapping initial="none">
                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
                <add source="(" target="\("/>
                <add source=")" target="\)"/>

    <!-- I'm not proud of it, but it is needed for workflows -->
    <xml name="wait_for">
        <param name="wait_for"
               label="Run this only after the following dataset is ready"
               help="Use this if you want to delay the job execution until some data is already loaded. The selected dataset will not be used for anything else."/>

    <xml name="feature_rel">
        <param name="rel_subject_re"
               label="Regular expression to extract the unique name of the parent feature"
               help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
            <expand macro="sanitized"/>

        <param name="rel_subject_type"
               label="Sequence type of the parent"
               help="this should be a Sequence Ontology term" />