Wrapping tools with optional data files

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Wrapping tools with optional data files

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">
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
    <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>
      <when value="advanced" >
    <param name="input_map" type="data" format="fasta" label="Fasta map file" optional="True" />

Is there another way around this?


Carrie Ganote

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