Re: [galaxy-dev] Variabels in label elements

23 Oct 2010

      Hi Jennifer,

sorry this doesn't work for me. If I use just the ${input} I get a reference to some memory location instead of the actual value. Therefore I was using the ${input.value_label} thing (on suggestion of the galaxy dev team :) ). But as mentioned this doesn't work for a conditional.
Below I have a sample tool_xml just to illustrate the current tool_config and what I want to do. Using it like this give me a history box with something like: "Tool output <galaxy.tools.Tool instance at 0x6c186c8>". Obvious this is not what I want. Also using ${cmd} or ${tol.cmd} or ${tool.value_label} don't work.
Any help or direction appreciated.
Alex

<tool id="testtool" name="test" version="0.1.alx" force_history_refresh="True">
  <description>: Var test</description>
  <command>
    /opt/someTooldir/$tool.cmd
        $input1
        #if $tool.cmd=="opt_2":
            -idr $tool.extra1
            -idq $tool.extra2
        #end if
        > $out_tool
  </command>
    <inputs>
      <conditional name="tool">
        <param name="cmd" type="select" label="Tool to run" help="blablabla" >
            <option value="opt_1">option1</option>
            <option value="opt_2">option2</option>
            <option value="opt_3">option3</option>
        </param>
        <when value="opt_2">
            <param name="extra1" type="text" value="0.05" label="IdR" />
            <param name="extra2" type="text" value="50" label="IdQ" />
        </when>
        <when value="opt_1" />
        <when value="opt_3" />
       </conditional>
      <param name="input1" type="data" format="tabular" label="MUMmer delta file" />
    </inputs>
    <outputs>
        <data name="out_tool" format="text" label="Tool output ${tool}" />
    </outputs>
    <requirements>
    </requirements>
    <tests>
        <test>
        </test>
    </tests>
    <help>
    </help>
    </help>
</tool>

________________________________________
Van: Jennifer Jackson [jen@bx.psu.edu]
Verzonden: vrijdag 22 oktober 2010 21:50
Aan: Bossers, Alex
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Variabels in label elements

Hi Alex,

Conditional usage/data return is possible, but not for the exact syntax
that you are using. Modifying the query by removing the ".value_label"
from the key should help:

change: ${input1.value_label}
to be: ${input1}

Please let us know if this works or not and we can help more from there,

Best,

Jen
Galaxy team

On 10/14/10 4:13 AM, Bossers, Alex wrote:
...
Hi All,
Does someone know how to get the value of a type="select" param_name displayed in the output file label?
I know how to do it if its just a non-nested param setup-up using ${input1.value_label} where the input1 is the select_name. But this fails if the select is inside a conditional..... From cheetah script I can call these values like IF $tool.cmd=="something":.....
But whatever I try in the<outputs><data>  fails (I though it to be ${tool.cmd.value_label} but that complains on cmd not defined.... All possible iteration tried :(
Snippet of a generalised tool.xml below.
Any suggestions or hints where to get documentation on this syntax is welcomed!
Alex
<command>
   /opt/tools/$tool.cmd
        $cmd_extra
        $input_delta
        #if $tool.cmd=="show-aligns":
              $tool.extra1
              $tool.extra2
        #end if
        >  $out_tool
   </command>
  <inputs>
    <conditional name="tool">
        <param name="cmd" type="select" value="show-snps" label="Select tool">
              <option value="show-snps">show snps</option>
              <option value="show-aligns">show aligns</option>
        </param>
   <when value="show-aligns">
         <param name="extra1" type="text" size="40" value="" label="IdR" help="FastA header ref sequence" />
         <param name="extra2" type="text" size="40" value="" label="IdQ" help="FastA header query sequence" />
        </when>
        <when value="show-snps" />
    </conditional>
   <param name="input_delta" type="data" format="tabular" label="MUMmer delta file" />
   <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="see specific cmd line options below for each tool" />
</inputs>
<outputs>
   <data name="out_tool" format="text" label="tool ${tool.cmd.value_label}" />
  </outputs>
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