view display_py.xml @ 1:33bb43de178f draft default tip

1st upload for print.py

<tool id="display_py" name="display_py" version="0.2" hidden="false" URL_method="post">
    <description>Use the display.py API browser from galaxy</description>

    <command>
    #if $__user_email__ in $__app__.config.admin_users
        #if str($add_path.question) == "yes"
            #if str($add_path.specific_path) == ""
                #if str($add_path.out_format) == "tsv"
                    $__root_dir__/scripts/api/display.py $api_key "$url_path_to_api/$content_type" | tail -n +3 |awk 'BEGIN{ FS="(\n|(name|id|[0-9]):)"; RS="#"; print "Num\tPath\tName\tID"; } /[:alnum:]/ { print NR-1,$2,$4,$6; }' > $display_py
                #elif str($add_path.out_format) == "txt"
                    $__root_dir__/scripts/api/display.py $api_key "$url_path_to_api/$content_type" > $display_py
                #else
                    print.py $__root_dir__/scripts/api/display.py $api_key "$url_path_to_api/$content_type" true > $display_py
                #end if
            #else
                #if str($add_content.content_id) == ""
                    #if str($add_path.out_format) == "txt"
                        $__root_dir__/scripts/api/display.py $api_key "$url_path_to_api/$content_type/$add_path.specific_path/contents" > $display_py
                    #else
                        print.py $__root_dir__/scripts/api/display.py $api_key "$url_path_to_api/$content_type/$add_path.specific_path/contents" false > $display_py
                    #end if
                #else
                    #if str($add_path.out_format) == "txt"
                        $__root_dir__/scripts/api/display.py $api_key "$url_path_to_api/$content_type/$add_path.specific_path/contents/$add_content.content_id" > $display_py
                    #else
                        print.py $__root_dir__/scripts/api/display.py $api_key "$url_path_to_api/$content_type/$add_path.specific_path/contents/$add_content.content_id" false > $display_py
                    #end if
                #end if
            #end if

        #else
            #if str($add_path.out_format) == "tsv"
                $__root_dir__/scripts/api/display.py $api_key "$url_path_to_api/$content_type" | tail -n +3 |awk 'BEGIN{ FS="(\n|(name|id|[0-9]):)"; RS="#"; print "Num\tPath\tName\tID"; } /[:alnum:]/ { print NR-1,$2,$4,$6; }' > $display_py
            #elif str($add_path.out_format) == "txt"
                $__root_dir__/scripts/api/display.py $api_key "$url_path_to_api/$content_type" > $display_py
            #else
                print.py $__root_dir__/scripts/api/display.py $api_key "$url_path_to_api/$content_type" true > $display_py
            #end if
        #end if
    #else
        print.py "Sorry, you are not an admin"
    #end if


    </command>

    <inputs>
        <param name="api_key" type="text" help="The user's API key (check your database)" optional="false">
        <!-- ${ __app__.model.User.get( $__user_id__ ).api_keys[0].key } -->
            <label>The user's key</label>
        </param>
        <param name="content_type" type="select" label="The content type">
            <option value="histories">histories</option>
            <option value="workflows">workflows</option>
            <option value="libraries">libraries</option>
        </param>
        <param name="url_path_to_api" type="baseurl" value="/api">
        </param>

        <conditional name="add_path">
            <param name="question" type="select" label="Add a specific path ID ?">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param name="specific_path" type="text" help="The ID to a specific [ workflow | history | library ]" optional="true">
                    <label>The galaxy specific id to access a [ workflow | history | library ]</label>
                </param>
                <param name="out_format" type="select" help="The output format (.tsv is available if there is no specific path)" label="The output format">
                    <option value="html">html</option>
                    <option value="txt">txt</option>
                </param>
            </when>
            <when value="no">
                <param name="out_format" type="select" help="The output format (.tsv is available if there is no specific path)" label="The output format">
                    <option value="tsv">tsv</option>
                    <option value="html">html</option>
                    <option value="txt">txt</option>
                </param>
            </when>
        </conditional>

        <conditional name="add_content">
            <param name="contents" type="boolean"  truevalue="true" falsevalue="false" label="View content (if you choose a specific ID previously.)">
            </param>
            <when value="true">
                <param name="content_id" type="text" help="The id of the specific content you want" optional="true">
                </param>
            </when>
            <when value="false">
                <param name="content_id" type="hidden" value="">
                </param>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data format="tabular" name="display_py" label="display.py API">
        <change_format>
            <when input="add_path.out_format" value="html" format="html" />
            <when input="add_path.out_format" value="txt" format="txt" />
            <when input="add_path.out_format" value="tsv" format="tabular" />
        </change_format>
    </data>
    </outputs>


    <help>

        display.py key url
         - key is the user's api key (see database. *Example : 8672ceeb5a3d5ac259fc7b0e741ecb9f* )
         - url is a concatenated string which is http://your_galaxy_url/api/[histories|workflows|libraries]/*eventually_something_more_specific*

----

**Details**

        This url string is created for you. All you have to do is to complete what you want and eventually the second part *eventually_something_more_specific*.

The content type of what you need could be:
         - histories
         - workflows
         - libraries

(...) And eventuelly, something more specific in the last input text box, to retrieve less (but more precise) information about a [workflow|history|library]:

         * 5e512af0e2dc10db
         * 5e512af0e2dc10db/contents
         * 5e512af0e2dc10db/contents/c4a2c33b2fb05347

    </help>
</tool>