annotate sendmail.xml @ 2:aff68aba2f62 draft

Replace XML with correct one. Apologies for the mistake

<tool id="sendemail" name="Send Mail On Completion" version="0.0.1">
  <description></description>
  <command interpreter="perl">
     sendmail.pl -u '$__user_email__' 

     ## subject
     #if $subjectfromselect.subjectsource == "typed" :
	#if $subjectfromselect.typedsubject != "":
          -s "${subjectfromselect.typedsubject}"
	#end if
     #elif $subjectfromselect.subjectsource == "other":
          -s "Galaxy Job Finished on ${subjectfromselect.subjectfile.display_name}"
     #elif $subjectfromselect.subjectsource == "input1":
	  -s "Galaxy Job Finished on ${input1.display_name}"
     #end if

     -d "${input1.display_name}@@@
     #for $q in $datafiles
          ${q.input2.display_name}@@@
     #end for
     "

     -o $output

	</command>
  <inputs>
	<conditional name="subjectfromselect">
	  <param name="subjectsource" type="select" label="Provide a Subject for the email :" help="If no subject is specified, a generic email will be send." >
		<option value="typed">Type the subject</option>
		<option value="input1">Base the subject on the first selected file</option>
		<option value="other">Base the subject on a file selected here</option>
	  </param>
 	  <when value="typed">
		<param name="typedsubject" type="text" size="25" label="Subject for email" />
	  </when>
	  <when value="other">
		<param name="subjectfile" type="data" label="Select a file from the history to base the subject upon" />
	  </when>
        </conditional>

    <param name="input1" type="data" label="Datafile to be completed:"/>
    <repeat name="datafiles" title="Data Files">
	<param name="input2" type="data" label="Select" />
    </repeat> 
  </inputs>
  <outputs>
    <data format="txt" name="output" label="Email Sent." hidden="true" />
  </outputs>

<help>
**What it does**

This tool sends an email to notify you when a certain analysis has finished. It takes any datfile(s) as input and sends the mail as soon as they are ready. Use it to notify you of workflow completion. In workflows, this can be set in the workflow editor, but this tools can be handy to get notifications for manually started jobs. 

**Input**

Datasets: 
Any dataset, or multiple datasets. They will be listed in the email. 

A subject:
You can specify the subject of the mail yourself, or use a datafile. In that case, the subject will be of the form "Galaxy Job Finished on Datafile_Name". If none is specified, you will just recieve a mail with "Galaxy workflow finished" as subject. 

**Output**

None. 

</help>

</tool>