optional tool arguments

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optional tool arguments

ryang
Hi - I'm implementing a new tool in Galaxy.  The tool either takes 1 or 2 fastq files as input.  If 1 file is specified, then 1 output file is created.  If 2 inputs are specified, then 2 output files will be created.  How do I specify the optional output parameter? 

I'm using this as my tool description right now:

<tool id="subsample_fastq" name="Random subsample">
  <description>a fastq file</description>
  <command>
    ### Check for optional input file
    #if strlen($fq2) > 0:
      RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2
    #else:
      RandomSubFq -w $readsRequested -i "$fq1" -o $out1
    #end if
  </command>
  <inputs>
    <param name="fq1" type="data" format="fastq" label="FASTQ file (1st of Pair)"/>
    <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd of Pair)" optional="true"/>
    <param name="readsRequested" type="integer" min="1" value="100000" label="Total number of reads you want from the file"/>
  </inputs>
  <outputs>
    <data format="fastq" name="out1" />
    <data format="fastq" name="out2" />
  </outputs>
  <stdio>
    <exit_code range="-1" level="fatal" description="RandomSubFq failed" />
  </stdio>



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Re: optional tool arguments

Hans-Rudolf Hotz
Hi Ryan

I guess you can work with filters, see:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set



Regards, Hans-Rudolf



On 04/28/2015 06:28 PM, Ryan G wrote:

> Hi - I'm implementing a new tool in Galaxy.  The tool either takes 1 or
> 2 fastq files as input.  If 1 file is specified, then 1 output file is
> created.  If 2 inputs are specified, then 2 output files will be
> created.  How do I specify the optional output parameter?
>
> I'm using this as my tool description right now:
>
> <tool id="subsample_fastq" name="Random subsample">
>    <description>a fastq file</description>
>    <command>
>      ### Check for optional input file
>      #if strlen($fq2) > 0:
>        RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2
>      #else:
>        RandomSubFq -w $readsRequested -i "$fq1" -o $out1
>      #end if
>    </command>
>    <inputs>
>      <param name="fq1" type="data" format="fastq" label="FASTQ file (1st
> of Pair)"/>
>      <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd
> of Pair)" optional="true"/>
>      <param name="readsRequested" type="integer" min="1" value="100000"
> label="Total number of reads you want from the file"/>
>    </inputs>
>    <outputs>
>      <data format="fastq" name="out1" />
>      <data format="fastq" name="out2" />
>    </outputs>
>    <stdio>
>      <exit_code range="-1" level="fatal" description="RandomSubFq failed" />
>    </stdio>
>
>
>
>
> ___________________________________________________________
> 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:
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>
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Re: optional tool arguments

Peter Cock
Yes, for example:
https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml

Peter

On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz <[hidden email]> wrote:

> Hi Ryan
>
> I guess you can work with filters, see:
>
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set
>
>
>
> Regards, Hans-Rudolf
>
>
>
>
> On 04/28/2015 06:28 PM, Ryan G wrote:
>>
>> Hi - I'm implementing a new tool in Galaxy.  The tool either takes 1 or
>> 2 fastq files as input.  If 1 file is specified, then 1 output file is
>> created.  If 2 inputs are specified, then 2 output files will be
>> created.  How do I specify the optional output parameter?
>>
>> I'm using this as my tool description right now:
>>
>> <tool id="subsample_fastq" name="Random subsample">
>>    <description>a fastq file</description>
>>    <command>
>>      ### Check for optional input file
>>      #if strlen($fq2) > 0:
>>        RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o
>> $out2
>>      #else:
>>        RandomSubFq -w $readsRequested -i "$fq1" -o $out1
>>      #end if
>>    </command>
>>    <inputs>
>>      <param name="fq1" type="data" format="fastq" label="FASTQ file (1st
>> of Pair)"/>
>>      <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd
>> of Pair)" optional="true"/>
>>      <param name="readsRequested" type="integer" min="1" value="100000"
>> label="Total number of reads you want from the file"/>
>>    </inputs>
>>    <outputs>
>>      <data format="fastq" name="out1" />
>>      <data format="fastq" name="out2" />
>>    </outputs>
>>    <stdio>
>>      <exit_code range="-1" level="fatal" description="RandomSubFq failed"
>> />
>>    </stdio>
>>
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>    https://lists.galaxyproject.org/
>>
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>>    http://galaxyproject.org/search/mailinglists/
>>
> ___________________________________________________________
> 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:
>  https://lists.galaxyproject.org/
>
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Re: optional tool arguments

ryang
Yes it took some experimenting but I finally figured it out.

Sent from my iPhone

> On Apr 29, 2015, at 4:51 AM, Peter Cock <[hidden email]> wrote:
>
> Yes, for example:
> https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml
>
> Peter
>
>> On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz <[hidden email]> wrote:
>> Hi Ryan
>>
>> I guess you can work with filters, see:
>>
>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set
>>
>>
>>
>> Regards, Hans-Rudolf
>>
>>
>>
>>
>>> On 04/28/2015 06:28 PM, Ryan G wrote:
>>>
>>> Hi - I'm implementing a new tool in Galaxy.  The tool either takes 1 or
>>> 2 fastq files as input.  If 1 file is specified, then 1 output file is
>>> created.  If 2 inputs are specified, then 2 output files will be
>>> created.  How do I specify the optional output parameter?
>>>
>>> I'm using this as my tool description right now:
>>>
>>> <tool id="subsample_fastq" name="Random subsample">
>>>   <description>a fastq file</description>
>>>   <command>
>>>     ### Check for optional input file
>>>     #if strlen($fq2) > 0:
>>>       RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o
>>> $out2
>>>     #else:
>>>       RandomSubFq -w $readsRequested -i "$fq1" -o $out1
>>>     #end if
>>>   </command>
>>>   <inputs>
>>>     <param name="fq1" type="data" format="fastq" label="FASTQ file (1st
>>> of Pair)"/>
>>>     <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd
>>> of Pair)" optional="true"/>
>>>     <param name="readsRequested" type="integer" min="1" value="100000"
>>> label="Total number of reads you want from the file"/>
>>>   </inputs>
>>>   <outputs>
>>>     <data format="fastq" name="out1" />
>>>     <data format="fastq" name="out2" />
>>>   </outputs>
>>>   <stdio>
>>>     <exit_code range="-1" level="fatal" description="RandomSubFq failed"
>>> />
>>>   </stdio>
>>>
>>>
>>>
>>>
>>> ___________________________________________________________
>>> 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:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>> ___________________________________________________________
>> 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:
>> https://lists.galaxyproject.org/
>>
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>> http://galaxyproject.org/search/mailinglists/
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