Issue writing functional tool test with repeat tag in config

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Issue writing functional tool test with repeat tag in config

Christy Shafer
Hello,

I'm trying to format a test tag in a tool config for the public Tool Shed that includes a repeated input parameter. I followed the syntax suggested in the following archived galaxy-dev post (was unable to find much other guidance): http://git.net/galaxy-development-source-control/msg15241.html, but the config file must be invalid because my repository on the Tool Shed does not register as an installable Galaxy utility. Any guidance is much appreciated.. Below are the relevant config code sections:

  <inputs>
        <repeat name="Files" title="Join file">
                <param name="joinMe" type="data" checked="yes" format="tabular" label="Join" />
                <param name="joinCol" label="using column" type="data_column" data_ref="joinMe" />
        </repeat>
        <param name="headerYes" type="select" label="Treat first line as header?">
                <option value="yes" selected="true">Yes</option>
                <option value="no">No</option>
        </param>
  </inputs>
  <outputs>
    <data format="tabular" name="Joined_all" label="Multi-Join result"/>
  </outputs>
  <tests>
     <test>
        <param name="Files_0|joinMe" value="multi_join_serial_in1.tab" ftype="tabular"/>
        <param name="Files_0|joinCol" value="1"/>
        <param name="Files_1|joinMe" value="multi_join_serial_in2.tab" ftype="tabular"/>
        <param name="Files_1|joinCol" value="1"/>
        <param name="Files_2|joinMe" value="multi_join_serial_in3.tab" ftype="tabular"/>
        <param name="Files_2joinCol" value="2"/>
        <param name="headerYes" value="yes"/>
        <output name="Joined_all" value="multi_join_serial_out.tab" ftype="tabular"/>
     <test/>
  <tests/>
 
Thanks for your help,
CS
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Re: Issue writing functional tool test with repeat tag in config

Daniel Blankenberg
Hi CS,

I assume you have the rest of the <tool> tags, but didn’t paste it here.

One thing is that you need to close your test and tests elements properly:
>     <test/>
>  <tests/>

    </test>
 </tests>

You may want to pass your config through a simple xml validator to try to shake any other issues out as well.



Thanks for using Galaxy,

Dan


On Apr 21, 2015, at 3:40 PM, Christy Shafer <[hidden email]> wrote:

> Hello,
>
> I'm trying to format a test tag in a tool config for the public Tool Shed that includes a repeated input parameter. I followed the syntax suggested in the following archived galaxy-dev post (was unable to find much other guidance): http://git.net/galaxy-development-source-control/msg15241.html, but the config file must be invalid because my repository on the Tool Shed does not register as an installable Galaxy utility. Any guidance is much appreciated.. Below are the relevant config code sections:
>
>  <inputs>
> <repeat name="Files" title="Join file">
> <param name="joinMe" type="data" checked="yes" format="tabular" label="Join" />
> <param name="joinCol" label="using column" type="data_column" data_ref="joinMe" />
> </repeat>
>        <param name="headerYes" type="select" label="Treat first line as header?">
>                <option value="yes" selected="true">Yes</option>
>                <option value="no">No</option>
>        </param>
>  </inputs>
>  <outputs>
>     <data format="tabular" name="Joined_all" label="Multi-Join result"/>
>  </outputs>
>  <tests>
>     <test>
> <param name="Files_0|joinMe" value="multi_join_serial_in1.tab" ftype="tabular"/>
> <param name="Files_0|joinCol" value="1"/>
> <param name="Files_1|joinMe" value="multi_join_serial_in2.tab" ftype="tabular"/>
> <param name="Files_1|joinCol" value="1"/>
> <param name="Files_2|joinMe" value="multi_join_serial_in3.tab" ftype="tabular"/>
> <param name="Files_2joinCol" value="2"/>
> <param name="headerYes" value="yes"/>
> <output name="Joined_all" value="multi_join_serial_out.tab" ftype="tabular"/>
>     <test/>
>  <tests/>
>
> Thanks for your help,
> CS
> ___________________________________________________________
> 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/
>

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Re: Issue writing functional tool test with repeat tag in config

Christy Shafer
Thanks, Dan; the Tool Shed accepted the repo as a valid utility now (big oops on my part). I had to make a few other corrections to the wrapper script as well, so we’ll see how the automated tool testing goes… Do you know how often testing is conducted on the site?

Thanks again,
C

On Apr 21, 2015, at 2:46 PM, Daniel Blankenberg <[hidden email]> wrote:

> Hi CS,
>
> I assume you have the rest of the <tool> tags, but didn’t paste it here.
>
> One thing is that you need to close your test and tests elements properly:
>>    <test/>
>> <tests/>
>
>    </test>
> </tests>
>
> You may want to pass your config through a simple xml validator to try to shake any other issues out as well.
>
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Apr 21, 2015, at 3:40 PM, Christy Shafer <[hidden email]> wrote:
>
>> Hello,
>>
>> I'm trying to format a test tag in a tool config for the public Tool Shed that includes a repeated input parameter. I followed the syntax suggested in the following archived galaxy-dev post (was unable to find much other guidance): http://git.net/galaxy-development-source-control/msg15241.html, but the config file must be invalid because my repository on the Tool Shed does not register as an installable Galaxy utility. Any guidance is much appreciated.. Below are the relevant config code sections:
>>
>> <inputs>
>> <repeat name="Files" title="Join file">
>> <param name="joinMe" type="data" checked="yes" format="tabular" label="Join" />
>> <param name="joinCol" label="using column" type="data_column" data_ref="joinMe" />
>> </repeat>
>>       <param name="headerYes" type="select" label="Treat first line as header?">
>>               <option value="yes" selected="true">Yes</option>
>>               <option value="no">No</option>
>>       </param>
>> </inputs>
>> <outputs>
>>   <data format="tabular" name="Joined_all" label="Multi-Join result"/>
>> </outputs>
>> <tests>
>>    <test>
>> <param name="Files_0|joinMe" value="multi_join_serial_in1.tab" ftype="tabular"/>
>> <param name="Files_0|joinCol" value="1"/>
>> <param name="Files_1|joinMe" value="multi_join_serial_in2.tab" ftype="tabular"/>
>> <param name="Files_1|joinCol" value="1"/>
>> <param name="Files_2|joinMe" value="multi_join_serial_in3.tab" ftype="tabular"/>
>> <param name="Files_2joinCol" value="2"/>
>> <param name="headerYes" value="yes"/>
>> <output name="Joined_all" value="multi_join_serial_out.tab" ftype="tabular"/>
>>    <test/>
>> <tests/>
>>
>> Thanks for your help,
>> CS
>> ___________________________________________________________
>> 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/
>>
>

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Issue writing functional tool test with repeat tag in config

Eric Rasche-2
Christy,

You may be interested in using planemo for local testing of tools, rather than waiting for the automated tool shed testing.


Cheers,
Eric


2015-04-21 15:25 GMT-05:00 Christy Shafer <[hidden email]>:
Thanks, Dan; the Tool Shed accepted the repo as a valid utility now (big oops on my part). I had to make a few other corrections to the wrapper script as well, so we’ll see how the automated tool testing goes… Do you know how often testing is conducted on the site?

Thanks again,
C

On Apr 21, 2015, at 2:46 PM, Daniel Blankenberg <[hidden email]> wrote:

> Hi CS,
>
> I assume you have the rest of the <tool> tags, but didn’t paste it here.
>
> One thing is that you need to close your test and tests elements properly:
>>    <test/>
>> <tests/>
>
>    </test>
> </tests>
>
> You may want to pass your config through a simple xml validator to try to shake any other issues out as well.
>
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Apr 21, 2015, at 3:40 PM, Christy Shafer <[hidden email]> wrote:
>
>> Hello,
>>
>> I'm trying to format a test tag in a tool config for the public Tool Shed that includes a repeated input parameter. I followed the syntax suggested in the following archived galaxy-dev post (was unable to find much other guidance): http://git.net/galaxy-development-source-control/msg15241.html, but the config file must be invalid because my repository on the Tool Shed does not register as an installable Galaxy utility. Any guidance is much appreciated.. Below are the relevant config code sections:
>>
>> <inputs>
>>      <repeat name="Files" title="Join file">
>>              <param name="joinMe" type="data" checked="yes" format="tabular" label="Join" />
>>              <param name="joinCol" label="using column" type="data_column" data_ref="joinMe" />
>>      </repeat>
>>       <param name="headerYes" type="select" label="Treat first line as header?">
>>               <option value="yes" selected="true">Yes</option>
>>               <option value="no">No</option>
>>       </param>
>> </inputs>
>> <outputs>
>>      <data format="tabular" name="Joined_all" label="Multi-Join result"/>
>> </outputs>
>> <tests>
>>    <test>
>>      <param name="Files_0|joinMe" value="multi_join_serial_in1.tab" ftype="tabular"/>
>>      <param name="Files_0|joinCol" value="1"/>
>>      <param name="Files_1|joinMe" value="multi_join_serial_in2.tab" ftype="tabular"/>
>>      <param name="Files_1|joinCol" value="1"/>
>>      <param name="Files_2|joinMe" value="multi_join_serial_in3.tab" ftype="tabular"/>
>>      <param name="Files_2joinCol" value="2"/>
>>      <param name="headerYes" value="yes"/>
>>      <output name="Joined_all" value="multi_join_serial_out.tab" ftype="tabular"/>
>>    <test/>
>> <tests/>
>>
>> Thanks for your help,
>> CS
>> ___________________________________________________________
>> 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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/



--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048


___________________________________________________________
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/