<filter> tag in output

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<filter> tag in output

Davide Cittaro
Hi all,
Apparently I cannot have the <filter> tag working for outputs in the small tool I'm wrinting:

<tool id="srf2fastq" name="SRF to FASTQ">
  <description>conversion</description>
  <command interpreter="sh">srf2fastq.sh $input1 $filter $paired $out_file1 $out_file2
  </command>
  <inputs>
    <param name="input1" type="data" format="srf" label="Select SRF Archive"/>
    <param name="filter" label="Filter out bad reads (QC fail)?" type="boolean" truevalue="Y" falsevalue="N" selected="True"/>
    <param name="paired" label="Is this Paired-end run?" type="boolean" truevalue="Y" falsevalue="N" selected="False"/>
  </inputs>
  <outputs>
      <data format="fastqillumina" name="out_file1"/>
      <data format="fastqillumina" name="out_file2">
         <filter>paired == "Y"</filter>
      </data>
  </outputs>
[…]
</tool>

According to the wiki pages, this syntax should enable the out_file2 if the "paired" checkbox is clicked... Unfortunately I always have the tool running as the checkbox wasn't checked (i.e. out_file2 is None). If I change the filter condition to paired=="N" I always have the tool running with two outputs...
Can anybody help me?

thanks

d


/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/




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Re: <filter> tag in output

Michael Siebauer
Change
<filter>paired == "Y"</filter>

to
<filter>paired is True</filter>


Cheers Michael ;-) 


Am 09.08.2010 16:23, schrieb Davide Cittaro:
Hi all,
Apparently I cannot have the <filter> tag working for outputs in the small tool I'm wrinting:

<tool id="srf2fastq" name="SRF to FASTQ">
  <description>conversion</description>
  <command interpreter="sh">srf2fastq.sh $input1 $filter $paired $out_file1 $out_file2
  </command>
  <inputs>
    <param name="input1" type="data" format="srf" label="Select SRF Archive"/>
    <param name="filter" label="Filter out bad reads (QC fail)?" type="boolean" truevalue="Y" falsevalue="N" selected="True"/>
    <param name="paired" label="Is this Paired-end run?" type="boolean" truevalue="Y" falsevalue="N" selected="False"/>
  </inputs>
  <outputs>
      <data format="fastqillumina" name="out_file1"/>
      <data format="fastqillumina" name="out_file2">
         <filter>paired == "Y"</filter>
      </data>
  </outputs>
[…]
</tool>

According to the wiki pages, this syntax should enable the out_file2 if the "paired" checkbox is clicked... Unfortunately I always have the tool running as the checkbox wasn't checked (i.e. out_file2 is None). If I change the filter condition to paired=="N" I always have the tool running with two outputs...
Can anybody help me?

thanks

d


/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: [hidden email]
*/




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Re: <filter> tag in output

Davide Cittaro
In reply to this post by Davide Cittaro

On Aug 9, 2010, at 4:23 PM, Davide Cittaro wrote:

Hi all,
Apparently I cannot have the <filter> tag working for outputs in the small tool I'm wrinting:


[…]

Can anybody help me?


Forget this... fixed

d
/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/



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