boolean type param (for an input tickbox) does not work correctly

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boolean type param (for an input tickbox) does not work correctly

Marina Gourtovaia
Hello

The boolean widget in the following tool config always works as if not
ticked while the select drop-down box in the same situation (teh
commented out xml) works ok. What's wrong with my tickbox?


<tool id="bam_to_fastq" name="BAM-to-FASTQ" version="1.0.0">
<requirements>
<requirement type="package">picard</requirement>
</requirements>
<description>converts BAM format to FASTQ format</description>
<command>
     java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/SamToFastq.jar
       VALIDATION_STRINGENCY=SILENT
       QUIET=true
       INPUT=$bam_in
       FASTQ=$fastq1_out
       #if $sPaired == "paired":
       SECOND_END_FASTQ=$fastq2_out
       #end if
</command>
<inputs>
<param name="sPaired" type="boolean" truevalue="paired"
falsevalue="single" checked="yes" label="Reads are paired" />
<!--<param name="sPaired" type="select" label="Is this library
mate-paired?">
<option value="single">Single-end</option>
<option value="paired">Paired-end</option>
</param>-->

<param name="bam_in" type="data" format="bam" label="BAM File to Convert" />
</inputs>
<outputs>
<data name="fastq1_out" format="fastqsanger" />
<data name="fastq2_out" format="fastqsanger" >
<filter>sPaired == "paired"</filter>
</data>
</outputs>
<tests>
</tests>
<help>
</help>
</tool>


Regards

Marina Gourtovaia


--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.
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Re: boolean type param (for an input tickbox) does not work correctly

Peter-2
On Wed, Dec 15, 2010 at 5:15 PM, Marina Gourtovaia <[hidden email]> wrote:

> Hello
>
> The boolean widget in the following tool config always works as if not
> ticked while the select drop-down box in the same situation (teh commented
> out xml) works ok. What's wrong with my tickbox?
>
>
> <tool id="bam_to_fastq" name="BAM-to-FASTQ" version="1.0.0">
> <requirements>
> <requirement type="package">picard</requirement>
> </requirements>
> <description>converts BAM format to FASTQ format</description>
> <command>
>    java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/SamToFastq.jar
>      VALIDATION_STRINGENCY=SILENT
>      QUIET=true
>      INPUT=$bam_in
>      FASTQ=$fastq1_out
>      #if $sPaired == "paired":
>      SECOND_END_FASTQ=$fastq2_out
>      #end if
> </command>

Just a guess, but have you tried this - based on similar issues
I had writing the NCBI BLAST+ wrappers:

#if str($sPaired) == "paired":
SECOND_END_FASTQ=$fastq2_out
#end if

The sPaired object isn't actually a string, its a proxy object with
the __str__ method defined.

Peter

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Re: boolean type param (for an input tickbox) does not work correctly

Marina Gourtovaia


On 15/12/2010 17:23, Peter wrote:

> On Wed, Dec 15, 2010 at 5:15 PM, Marina Gourtovaia<[hidden email]>  wrote:
>> Hello
>>
>> The boolean widget in the following tool config always works as if not
>> ticked while the select drop-down box in the same situation (teh commented
>> out xml) works ok. What's wrong with my tickbox?
>>
>>
>> <tool id="bam_to_fastq" name="BAM-to-FASTQ" version="1.0.0">
>> <requirements>
>> <requirement type="package">picard</requirement>
>> </requirements>
>> <description>converts BAM format to FASTQ format</description>
>> <command>
>>     java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/SamToFastq.jar
>>       VALIDATION_STRINGENCY=SILENT
>>       QUIET=true
>>       INPUT=$bam_in
>>       FASTQ=$fastq1_out
>>       #if $sPaired == "paired":
>>       SECOND_END_FASTQ=$fastq2_out
>>       #end if
>> </command>
> Just a guess, but have you tried this - based on similar issues
> I had writing the NCBI BLAST+ wrappers:
>
> #if str($sPaired) == "paired":
> SECOND_END_FASTQ=$fastq2_out
> #end if
>
> The sPaired object isn't actually a string, its a proxy object with
> the __str__ method defined.
>
> Peter

Thanks a lot for the tip, Peter. Also, had to use a different filter
expression (sPaired is True)

BTW, I am making a wrapper around Picard
http://picard.sourceforge.net/command-line-overview.shtml#Overview. Is
there enough interest to this to submit this to the core Galaxy? In
Sanger, our Illumina pipeline end up with BAM files, so the end users
need a BAM-FASTQ converter, hence this binding I am making

Marina Gourtovaia


--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.
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Re: boolean type param (for an input tickbox) does not work correctly

Peter-2
On Thu, Dec 16, 2010 at 1:48 PM, Marina Gourtovaia <[hidden email]> wrote:
>
> Thanks a lot for the tip, Peter. Also, had to use a different filter
> expression (sPaired is True)

Great.

> BTW, I am making a wrapper around Picard
> http://picard.sourceforge.net/command-line-overview.shtml#Overview. Is there
> enough interest to this to submit this to the core Galaxy? In Sanger, our
> Illumina pipeline end up with BAM files, so the end users need a BAM-FASTQ
> converter, hence this binding I am making

I'm sure a Picard wrapper would be useful. For this particular case,
BAM to unaligned FASTQ you may have other options. I'd take a
look at pysam, the Python wrapper for the samtools C API if I were
you, but then I don't speak Java ;)

Also EMBOSS has some BAM support nowadays, and I've got some
experimental code on a Biopython branch which was partly written
for recovering unaligned paired end FASTQ files from BAM in order
to remap them to a different reference.

Peter
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Re: boolean type param (for an input tickbox) does not work correctly

Anton Nekrutenko
In reply to this post by Marina Gourtovaia
Marina:

Yes, these would be very useful. PLease consider committing them to Galaxy Tool Shed at http://usegalaxy.org/community

Thanks!

anton





BTW, I am making a wrapper around Picard http://picard.sourceforge.net/command-line-overview.shtml#Overview. Is there enough interest to this to submit this to the core Galaxy? In Sanger, our Illumina pipeline end up with BAM files, so the end users need a BAM-FASTQ converter, hence this binding I am making


Anton Nekrutenko




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