Tool wrapper NotFound error

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Tool wrapper NotFound error

evan clark
I have written  the below tool wrapper and when running in galaxy I
receive the error. I am not sure the issue with the wrapper.
~~~~

Traceback (most recent call last):
   File
"/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py",
line 170, in prepare_job
     job_wrapper.prepare()
   File
"/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py",
line 897, in prepare
     self.command_line, self.extra_filenames, self.environment_variables
= tool_evaluator.build()
   File
"/home/eclark28/galaxy_production/galaxy/lib/galaxy/tools/evaluation.py", line
445, in build
     raise e
NotFound: cannot find 'library'

~~~~

~~~~
<tool id="miso" name="Miso" version="1.0.0">

<description>Alternative splicing analysis</description>

<version_command>python
/home/eclark28/galaxy_production/python/lib/python2.7/site-packages/misopy/miso.py
--version

</version_command>

<command>

<![CDATA[

    mkdir -p '${output.files_path}/indexed_gff' &&
    mkdir -p '${output.files_path}/exonUtil' &&
    mkdir -p '${output.files_path}/pe' &&
    mkdir -p '${output.files_path}/miso' &&


   ~/galaxy_production/python/bin/index_gff
       --index
       '${input_gff}'
       '${output.files_path}/indexed_gff'
   #if str( $library.type ) == "paired":
&& /home/eclark28/galaxy_production/python/bin/exon_utils
       --get-const-exons
       '${master_input_gff}'
       --min-exon-size '${exon_size}'
       --output-dir '${output.files_path}/exonUtil'
&&   ~/galaxy_production/python/bin/pe_utils
       --compute-insert-len
       '${bam_file}'
         
'${output.files_path}/exonUtil/${master_input_gff}.min_${exon_size}.const_exons.gff'

        --output-dir '${output.files_path}/pe'

   #end if
&& python
/home/eclark28/galaxy_production/python/lib/python2.7/site-packages/misopy/miso.py

       --run
       '${output.files_path}/indexed_gff'
       '${bam_file}'
       --output-dir '${output.files_path}/miso'
       --read-len '${read_length}'
       #if str( $library.type ) == "paired":
       --paired-ended
`'${output.files_path}/pe/insert-dist/${master_input_gff}.insert_len' |
parseExonUtil.pl`
       #end  if
       --use-cluster && tree -H ./ ${output}







   ]]>

</command>

<inputs>

<section name="basicOptions" title="Basic Options" expanded="True">
<!-- <param name="indexed_gff" type="data" label="Indexed GFF File" /> -->
<param name="bam_file" type="data" label="BAM File" />
<param name="input_gff" type="data" label="Input GFF" />
<param name="exon_size" type="integer" label="Exon Size" value="1000" />
<param name="read_length" type="integer" label="Read Length" value="99" />
<conditional name="library">
<param name="type" type="select" label="Is this single or paired library">
<option value="single">Single-end</option>
<option value="paired">Paired-end</option>
</param>

<when value="paired">
<param name="master_input_gff" type="data" label="Master GFF" />
</when>
<when value="single">

</when>
</conditional>
</section>
</inputs>

<outputs>

<data format="html" name="output"  />





</outputs>

</tool>
~~~~
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Re: Tool wrapper NotFound error

John Chilton-4
It looks like your library conditional is wrapped in a section called
"basicOptions". For this reason when it appears in your <command>
block you need to use $basicOptions.library.type for instance instead
of $library.type. Hope this helps and thanks for using Galaxy!

-John

On Wed, Oct 26, 2016 at 11:39 AM, evan clark <[hidden email]> wrote:

> I have written  the below tool wrapper and when running in galaxy I receive
> the error. I am not sure the issue with the wrapper.
> ~~~~
>
> Traceback (most recent call last):
>   File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py",
> line 170, in prepare_job
>     job_wrapper.prepare()
>   File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line
> 897, in prepare
>     self.command_line, self.extra_filenames, self.environment_variables =
> tool_evaluator.build()
>   File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/tools/evaluation.py",
> line 445, in build
>     raise e
> NotFound: cannot find 'library'
>
> ~~~~
>
> ~~~~
> <tool id="miso" name="Miso" version="1.0.0">
>
> <description>Alternative splicing analysis</description>
>
> <version_command>python
> /home/eclark28/galaxy_production/python/lib/python2.7/site-packages/misopy/miso.py
> --version
>
> </version_command>
>
> <command>
>
> <![CDATA[
>
>    mkdir -p '${output.files_path}/indexed_gff' &&
>    mkdir -p '${output.files_path}/exonUtil' &&
>    mkdir -p '${output.files_path}/pe' &&
>    mkdir -p '${output.files_path}/miso' &&
>
>
>   ~/galaxy_production/python/bin/index_gff
>       --index
>       '${input_gff}'
>       '${output.files_path}/indexed_gff'
>   #if str( $library.type ) == "paired":
> && /home/eclark28/galaxy_production/python/bin/exon_utils
>       --get-const-exons
>       '${master_input_gff}'
>       --min-exon-size '${exon_size}'
>       --output-dir '${output.files_path}/exonUtil'
> &&   ~/galaxy_production/python/bin/pe_utils
>       --compute-insert-len
>       '${bam_file}'
>
> '${output.files_path}/exonUtil/${master_input_gff}.min_${exon_size}.const_exons.gff'
>        --output-dir '${output.files_path}/pe'
>
>   #end if
> && python
> /home/eclark28/galaxy_production/python/lib/python2.7/site-packages/misopy/miso.py
>       --run
>       '${output.files_path}/indexed_gff'
>       '${bam_file}'
>       --output-dir '${output.files_path}/miso'
>       --read-len '${read_length}'
>       #if str( $library.type ) == "paired":
>       --paired-ended
> `'${output.files_path}/pe/insert-dist/${master_input_gff}.insert_len' |
> parseExonUtil.pl`
>       #end  if
>       --use-cluster && tree -H ./ ${output}
>
>
>
>
>
>
>
>   ]]>
>
> </command>
>
> <inputs>
>
> <section name="basicOptions" title="Basic Options" expanded="True">
> <!-- <param name="indexed_gff" type="data" label="Indexed GFF File" /> -->
> <param name="bam_file" type="data" label="BAM File" />
> <param name="input_gff" type="data" label="Input GFF" />
> <param name="exon_size" type="integer" label="Exon Size" value="1000" />
> <param name="read_length" type="integer" label="Read Length" value="99" />
> <conditional name="library">
> <param name="type" type="select" label="Is this single or paired library">
> <option value="single">Single-end</option>
> <option value="paired">Paired-end</option>
> </param>
>
> <when value="paired">
> <param name="master_input_gff" type="data" label="Master GFF" />
> </when>
> <when value="single">
>
> </when>
> </conditional>
> </section>
> </inputs>
>
> <outputs>
>
> <data format="html" name="output"  />
>
>
>
>
>
> </outputs>
>
> </tool>
> ~~~~
> ___________________________________________________________
> 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/