view DockerToolFactory.xml @ 0:0fa46413d0d9 draft

planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="rgTF" name="docker_tool_factory" version="0.1.3">
    <description>Makes scripts into tools using Docker</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="9.10">ghostscript</requirement>
        <requirement type="package" version="1.3.20">graphicsmagick</requirement>
        <requirement type="package" version="0.4.0">docker-py</requirement>
    </requirements>
    <command interpreter="python"><![CDATA[
        DockerToolFactory.py --script_path "$runme" --interpreter "$interpreter"
        --tool_name "$tool_name" --user_email "$__user_email__"
        #if $generate_simple_output.make_TAB=="yes":
        --output_tab "$tab_file"
        #end if
        #if $makeMode.make_Tool=="yes":
        #if generate_simple_output.make_TAB=="yes":
        --output_format "$out_format"
        #end if
        --make_Tool "$makeMode.make_Tool"
        --tool_desc "$makeMode.tool_desc"
        --tool_version "$makeMode.tool_version"
        --new_tool "$new_tool"
        --help_text "$helpme"
        #if $make_HTML.value=="yes":
        --include_dependencies "${makeMode.include_deps}"
        #end if
        #end if
        #if $make_HTML.value=="yes":
        --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
        #else:
        --output_dir "."
        #end if
        #if $additional_parameters != 'None':
        #for i in $additional_parameters:
        --additional_parameters
        "$i.param_name, $i.param_value"
        #end for
        #end if
        #if $input_files != 'None':
        --input_tab
        #for i in $input_files:
        $i.input
        #end for
        #for i in $input_files:
        --input_format
        #if str($i.in_format) == "None":
        "Any"
        #else
        "$i.in_format"
        #end if
        #end for
        #end if
        ]]>
    </command>
    <configfiles>
        <configfile name="runme">$dynScript</configfile>
        <configfile name="helpme">
            #if $makeMode.make_Tool == "yes":
            ${makeMode.help_text}
            #end if
        </configfile>
    </configfiles>
    <inputs>
        <repeat name="input_files" title="Select input files">
            help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
            <param name="in_format" type="select" optional="true" multiple="true"
                   label="Optional: Select the allowed input datatype(s) for your tool/script">
                <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
                    <column name="value" index="0"/>
                </options>
            </param>
        </repeat>
        <repeat name="additional_parameters" title="Set additional parameters">
            <param name="param_name" type="text" value="parameter_name" label="Choose a parameter name" size="20">
                <sanitizer invalid_char="">
                    <valid initial="string.letters,string.digits">
                        <add value="@_."/>
                    </valid>
                    >
                </sanitizer>
            </param>
            <param name="param_value" type="text" value="parameter_value" label="Enter a parameter value" size="50">
                <sanitizer>
                    <valid initial="string.printable">
                    </valid>
                    <mapping initial="none"/>
                </sanitizer>
            </param>
        </repeat>
        <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs"
               size="60"
               help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
            <sanitizer invalid_char="">
                <valid initial="string.printable"/>
            </sanitizer>
        </param>
        <conditional name="makeMode">
            <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry"
                   help="Ready to deploy securely!" size="60">
                <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
                <option value="" selected="true">No. Just run the script please</option>
            </param>
            <when value="yes">
                <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses"
                       type="text" value="0.01"
                       help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
                <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
                       help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)"/>
                <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
                       size="8x120" value="**What it Does**"
                       help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html">
                    <sanitizer>
                        <valid initial="string.printable">
                        </valid>
                        <mapping initial="none"/>
                    </sanitizer>
                </param>
                <param name="include_deps" type="select"
                       label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
                       help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
                    <option value="">Rely on system ghostscript and graphicsmagick rather than include these as
                        dependencies
                    </option>
                    <option value="yes" selected="true">Include dependencies so target installations will always work if
                        HTML is being generated
                    </option>
                </param>

            </when>
            <when value="">
            </when>
        </conditional>
        <param name="out_format" type="text" value="txt" hidden="True"/>
        <param name="make_HTML" type="select"
               label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
               help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
            <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
            <option value="" selected="true">No, no HTML output file thanks</option>
        </param>
        <conditional name="generate_simple_output">
            <param name="make_TAB" type="select"
                   label="Create a new history output alongside the HTML file specified above"
                   help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
                <option value="yes" selected="true">My script writes to a new history output</option>
                <option value="no">I do not want a new history output file</option>
            </param>
            <when value="yes">
                <param name="out_format" type="select" label="Select the datatype that your tool/script produces"
                       help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" optional="True">
                    <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
                        <column name="value" index="0"/>
                    </options>
                </param>
            </when>
            <when value="no">
                 <param name="out_format" type="text" value="txt" optional="True" hidden="True"/>
            </when>
        </conditional>
        <param name="interpreter" type="select" label="Select the interpreter for your code">
            <option value="Rscript" selected="true">Rscript</option>
            <option value="python">python</option>
            <option value="perl">perl</option>
            <option value="sh">sh</option>
        </param>
        <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True"
               size="8x120"
               help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None').">
            <sanitizer>
                <valid initial="string.printable">
                </valid>
                <mapping initial="none"/>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <!--  <data format_source="input" name="tab_file" label="${tool_name}.${out_format}"> -->
        <data format_source="input" name="tab_file">
            <filter>generate_simple_output['make_TAB'] == "yes"</filter>
            <actions>
                <action type="format">
                    <option type="from_param" name="out_format"/>
                </action>
            </actions>
        </data>
        <data format="html" name="html_file" label="${tool_name}.html">
            <filter>make_HTML == "yes"</filter>
        </data>
        <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
            <filter>makeMode['make_Tool'] == "yes"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="interpreter" value="Rscript"/>
            <param name="make_HTML" value="yes"/>
            <param name="generate_simple_output|makeTAB" value="no"/>
            <param name="out_format" value="txt"/>
	    <param name="dynScript" value="for (i in 1:10) {; foo = runif(100); bar = rnorm(100); bar = foo + bar; pdf(&quot;anotherplot.pdf&quot;); plot(1,2); dev.off();}"/>
            <output name="html_file" file="html_output/My_dynamic_script_html.html" compare="diff"/>
        </test>
    </tests>
    <expand macro="help_macro"/>
</tool>