view submit_to_mogi.xml @ 6:187641a876b9 draft default tip

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty

<tool id="submit_to_mogi" name="submit_to_mogi" version="0.0.3">
    <description>
        Submit Galaxy datasets to MOGI django database
    </description>


    <macros>
        <import>macros.xml</import>
    </macros>

   
 <stdio>
        <exit_code range="1:" />
    </stdio>
     <command>
       #set $galaxy_data_id=$__app__.security.encode_id($mogi_data.id)
       #set $galaxy_history_id=$__app__.security.encode_id($mogi_data.creating_job.history.id)
       #set $galaxy_history_name=$mogi_data.creating_job.history.name
       curl -X POST --insecure $mogi_url/mogi/rest/incoming_galaxy_data/ -d galaxy_data_id=$galaxy_data_id 
                    -d galaxy_history_id=$galaxy_history_id -d galaxy_history_name='$galaxy_history_name' 
                    -d galaxy_name=$galaxy_name -d investigation_name=$investigation_name -d galaxy_url=$galaxy_url > curl_out.txt;
      </command>
    <inputs>


        <param type="data" name="mogi_data" label="Data to submit to MOGI" format="sqlite"
               help="SQLite database to submit to MOGI" />


        <param type="text" name="mogi_url" label="MOGI URL" 
               help="URL for MOGI" />

        <param type="text" name="galaxy_name" label="Name of Galaxy instance in MOGI"
               help="Should be lower cases with no white spaces or non alphnumeric characters except _ or -" />

        <param type="text" name="investigation_name" label="Name of the investigation in submit to in MOGI"
               help="Should be lower cases with no white spaces or non alphnumeric characters except _ or -" />
  
         <param type="text" name="galaxy_url" label="Galaxy URL"
               help="URL of the Galaxy site (not required, but useful for a reference)" />


	
    </inputs>
    <outputs>
        <data name="curl_out" format="json" label="${tool.name} on ${on_string}: submit to MOGI (json if successful)"
              from_work_dir="curl_out.txt" />

    </outputs>
    <tests>
        <test>
	    
            <param name="mogi_data" value="alldata.sqlite"/>
            <param name="mogi_url" value="https://www.djangoproject.com/"/>
           
            <output name="curl_out" >
        	    <assert_contents>
		       <has_text_matching expression=".*django.*" />
		    </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[
=============================================================
Submit SQLite Database to MOGI
=============================================================


-----------
Output
-----------
* out.json: The JSON request sent to MOGI

  ]]></help>
<expand macro="citations" />
</tool>