annotate macros.xml @ 0:9512201417a5 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de

<macros>
    <xml name="command_macro">
        <command detect_errors="aggressive"><![CDATA[
            #import re
            mkdir inputs &&
            #for $p in $parameters
                #if $p.type_cond.type_sel == "data"
                    #if $p.type_cond.filename != ''
                        #set fname = $p.type_cond.filename
                    #else
                        #set fname=re.sub('[^\s\w\.]', '_', str($p.type_cond.param.element_identifier)) + "." + $p.type_cond.param.ext
                    #end if
                    ln -s '$p.type_cond.param' inputs/'$fname' &&
                #end if
            #end for

            @COMMAND_AND_SETUP@
            '$script'
            #for $p in $parameters
                #if $p.type_cond.type_sel == "data"
                    #if $p.type_cond.filename != ''
                        #set fname = $p.type_cond.filename
                    #else
                        #set fname=re.sub('[^\s\w\.]', '_', str($p.type_cond.param.element_identifier)) + "." + $p.type_cond.param.ext
                    #end if
                    inputs/'$fname'
                #else
                    '$p.type_cond.param'
                #end if
            #end for
        ]]></command>
        <configfiles>
            <configfile name="script">$code</configfile>
        </configfiles>
    </xml>
    <xml name="inputs_macro">
        <inputs>
            <repeat name="parameters" title="Parameters" min="1" default="1" help="Supply one or more parameters">
                <conditional name="type_cond">
                    <param name="type_sel" type="select" label="Parameter type">
                        <option value="data">Dataset</option>
                        <option value="text">Text</option>
                        <!-- Not sure if int/float make sense .. can they be connected to text in WFs? -->
                    </param>
                    <when value="data">
                        <param name="param" type="data" label="Dataset"/>
                        <param name="filename" type="text" label="File name" help="Set if you want to access the data set with a specific file name. Only alphanumeric characters, dash and underscore are allowed (all other characters are replaced by an undercore). Default is Galaxy's data set name.">
                            <sanitizer invalid_char="_">
                                <valid initial="string.ascii_letters,string.digits">
                                    <add value="_" />
                                    <add value="-" />
                                    <add value="." />
                                </valid>
                            </sanitizer> 
                            <!-- file names must not start with dash -->
                            <validator type="regex" negate="true" message="Filenames must not start with a dash">^[-].*$</validator>
                        </param>
                    </when>
                    <when value="text">
                        <param name="param" type="text" label="Text parameter" help=""/>
                    </when>
                </conditional>
            </repeat>
            <param name="code" type="text" area="true" label="@LANGUAGE@ program" help="">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
            </param>
        </inputs>
    </xml>
    <xml name="outputs_macro">
        <outputs>
            <collection name="output" type="list" label="Outputs">
                <discover_datasets pattern="__designation_and_ext__"/>
            </collection>
        </outputs>
    </xml>

    <xml name="help_macro">
        <help><![CDATA[
**Warning**

.. class:: warningmark

**Make sure that you know what you are doing. When used wrong the tool may lead to
data loss of files that you can write to.**

.. class:: warningmark

This tool is only intended to serve for single-use, ad-hoc exploratory analysis
of data sets with small @LANGUAGE@ scripts.

.. class:: warningmark

If you use this tool repeatedly with the same script and/or have the impression
that other Galaxy users could profit from this script then contact your local
Galaxy administrator or the Galaxy community, e.g. at https://github.com/galaxyproject/tools-iuc/,
and ask if your script can be turned into a proper Galaxy tool.
One of the main advantages of a proper Galaxy tool is that they are tested and
maintained. Furthermore the whole Galaxy community may profit.

**What it does**

Executes an **@LANGUAGE@** script (in a @CONTAINER@ container).

An arbitrary number of data or text parameters can be given to the script.
Data parameters are by default named like the datasets name and the datatype
is used as extension. This can be overwritten with the filename parameter
for the corresponding dataset.

@HELP_PARAMETERS@

@HELP_READ_FROM_STDIN@

Output datasets are read from the current working directory and put into a
single collection.  The collection elements will be named as the file names
(without the extension). The file extension determines the datatype of the
datasets (or Galaxy will try to autodetect the data type).
        ]]></help>
    </xml>
</macros>