comparison gmql_rest_repository.xml @ 0:bb858d9ad271 draft default tip

planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty

0:bb858d9ad271

<tool id="gmql_repository" name="GMQL Repository Access" version="0.1.1">
    <description>View, browse, rename or delete datasets in the user's space on the GMQL system.</description>
    <macros>
        <import>gmql_rest_macros.xml</import>
    </macros>
    <command><![CDATA[
        python $__tool_directory__/gmql_rest_datasets.py
        #set $cmd = $rep.operation
        #if $cmd == 'list' :
         $out_list
        #elif $cmd == 'samples' :
         $out_samples
         -dataset=$rep.ds_name
        #elif $cmd == 'delete' :
         $updated_list
         -dataset=$rep.dataset_del
        #elif $cmd == 'rename' :
         $updated_list
         -dataset=$rep.dataset_ren
         -new_name=$rep.new_name
        #end if
        -user=$authToken
        -cmd=$cmd
    ]]></command>
    <code file="dynamic_utils.py">
        <hook validate_input="validate" />
    </code>
    <inputs>
        <param format="gmql_user" name="authToken" type="data" label="Select user" />
        <conditional name="rep">
            <param name="operation" type="select" display="radio" multiple="false" label="Select the desired action" >
            <option value="list">View datasets</option>
            <option value="samples">View a dataset's samples</option>
            <option value="rename">Rename a dataset</option>
            <option value="delete">Delete a dataset</option>
        </param>
            <when value="list">
                <!-- do nothing -->
            </when>
            <when value="samples">
                <param name="gmql_datasets" type="data" format="gmql_repository" label="Working Datasets"/>
                <param name="ds_name" type="select" label="Select Dataset">
                    <options from_dataset="gmql_datasets">
                        <column name="value" index="0"/>
                    </options>
                </param>

            </when>
            <when value="rename">
                <param name="gmql_datasets" type="data" format="gmql_repository" label="Working Datasets" />
                <param name="dataset_ren" type="select" label="Select Dataset to rename">
                    <options from_dataset="gmql_datasets">
                        <column name="value" index="0" />
                        <filter column="1" type="static_value" value="public" keep="false" />
                    </options>
                </param>
                <param name="new_name" type="text" label="New Dataset Name" >
		            <validator type="regex" message="Only alphanumeric characters and underscore are allowed">[\w]+$</validator>
	            </param>
            </when>
            <when value="delete">
                <param name="gmql_datasets" type="data" format="gmql_repository" label="Working Datasets" />
	            <param name="dataset_del" type="select" label="Select Dataset to delete">
		            <options from_dataset="gmql_datasets">
                            <column name="value" index="0" />
                            <filter column="1" type="static_value" value="public" keep="false"/>
		            </options>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="gmql_repository" name="out_list" label="${authToken.name.split()[0].rstrip('')} GMQL Datasets">
            <filter>rep['operation'] == 'list'</filter>
            <actions>
                <action name="column_names" type="metadata" default="dataset,owner" />
            </actions>
        </data>
        <data format="tabular" name="out_samples" label="${rep.ds_name} samples list from ${authToken.name.split()[0].rstrip('')} GMQL Datasets" >
            <filter>rep['operation'] == 'samples'</filter>
            <actions>
                <action name="column_names" type="metadata" default="id,sample,ext" />
            </actions>
        </data>
       <data format="gmql_repository" name="updated_list" label="${authToken.name.split()[0].rstrip('')} GMQL Datasets">
            <filter>rep['operation'] == 'rename' or rep['operation'] == 'delete'</filter>
            <actions>
                <action name="column_names" type="metadata" default="dataset,owner" />
            </actions>
       </data>
    </outputs>
    <tests>
        <test>
            <param name="authToken" value="guest.gmql_user" />
            <conditional name="rep">
                <param name="operation" value="list" />
            </conditional>
            <output name="out_list" ftype="gmql_repository">
                <assert_contents>
                    <has_n_columns n="2" />
                    <has_line_matching expression="Example_Dataset_1\tpublic" />
                    <has_line_matching expression="Example_Dataset_2\tpublic" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="authToken" value="guest.gmql_user" />
            <conditional name="rep">
                <param name="operation" value="samples" />
                <param name="gmql_datasets" value="rep.gmql_repository" />
                <param name="ds_name" value="Example_Dataset_1" />
            </conditional>
            <output name="out_samples" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="3" />
                    <has_text text="S_00000" />
                    <has_text text="S_00001" />
                    <has_text text="S_00002" />
                    <has_text text="S_00003" />
                    <has_text text="S_00004" />
                    <has_text text="S_00005" />
                    <has_text text="S_00006" />
                </assert_contents>
            </output>
        </test>
    </tests>
  <help>
This tool serves to access the GMQL public repository, and the user’s private one.
In particular, within the public repository interesting datasets collected from established sources,
like ENCODE or UCSC, and small example datasets are hosted.

----

**What it does**

- **view datasets**: list all datasets, both private and public
- **view dataset's samples**: list samples of given dataset
- **rename dataset**: change name of dataset, return updated datasets list
- **delete dataset**: delete dataset, return updated dataset list

.. class:: warningmark

Public datasets can only be seen or browsed, but not renamed or deleted.

.. class:: warningmark

A gmql_user authentication token is required for every action.
  </help>
  <expand macro="citations" />
</tool>