Wrapping tools with optional data files

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Wrapping tools with optional data files

cganote@iu.edu
Hi List,

I am wrapping a Galaxy tool for the GFFread utility from Cufflinks. It has a few optional files as inputs, but I can't get this to translate to the tool wrapper.
I started with a tool that has an advanced options menu. When this is selected as "advanced", it brings up a bunch of parameters, including the optional fasta file. If I select something for the optional field, it works fine; if I don't select anything (it says "Selection is Optional"), I get this error and the tool doesn't run:
Error executing tool: 'param name'
If I use the basic options, it works fine. This seems to have nothing to do with the <command> tag, which can never mention the param name.

I looked for an example of a successful optional file tool and found the GATK depth of coverage tool. It doesn't have that conditional tag around its optional file, though - and when I add the advanced options conditional, it breaks it.
Here's the prototype:
<tool id="gffread" name="GFFread" version="0.0.1">
<command>
gffread $input_file -o $output_file
#if $adv_opts.adv_opts_selector == "advanced":
#if str( $adv_opts.input_map ) != "None":
-g $adv_opts.input_map
#end if
#end if
</command>
  <inputs>
    <param name="input_file" type="data" format="gff,gtf,gff3" label="GFF file"/>
    <param name="works" type="data" format="fasta" label="This one works" optional="True" />
    <conditional name="adv_opts">
      <param name="adv_opts_selector" type="select" label="Advanced Options">
    <option value="basic" selected="True">Hide Advanced Options</option>
    <option value="advanced">Show Advanced Options</option>
      </param>
      <when value="advanced" >
    <param name="input_map" type="data" format="fasta" label="Fasta map file" optional="True" />
      </when>
    </conditional>
  </inputs>
...

Is there another way around this?

Thanks,

Carrie Ganote

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/