Custom Wrapper unable to find 'read

Question: Custom Wrapper unable to find 'read_length'

2.1 years ago by

djevo1 • 60

djevo1 • 60 wrote:

I have designed the following wrapper for a tool, however galaxy is giving the error Cannot Find: 'read_type' I am not sure what the issue with it is.

<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($read_type) == "paired":
  && /home/eclark28/galaxy_production/python/bin/exon_utils
    --get-const-exons                                                
      '${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($read_type) == "paired":
      --paired-ended `'${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="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 Lenth" value="99" />
    <conditional name="library">
        <param name="read_type" type="select" label="Are the reads single or paired-end?">
          <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>

rna-seq galaxy wrapper • 635 views

ADD COMMENT • link •

modified 2.1 years ago by y.hoogstrate • 460 • written 2.1 years ago by djevo1 • 60

galaxy.jobs.runners ERROR 2016-10-26 10:49:47,731 (313) Failure preparing job
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'

ADD REPLY • link written 2.1 years ago by djevo1 • 60

2.1 years ago by

y.hoogstrate • 460

Netherlands

y.hoogstrate • 460 wrote:

I think it will work if you use ${library.read_type} (name of the conditional)?

ADD COMMENT • link written 2.1 years ago by y.hoogstrate • 460

That didn't work. It generates the same issue.

ADD REPLY • link written 2.1 years ago by djevo1 • 60

I did not look carefully enough and I missed the section element. I think it should be ${basicOptions.library.read_type}.

ADD REPLY • link written 2.1 years ago by y.hoogstrate • 460

That fixed the first issue, now I am getting the same issue with master_input_gff

ADD REPLY • link written 2.1 years ago by djevo1 • 60

It's exactly the same problem. Please take a careful look at my last reply and you'll be able to solve it immediately ;-)

ADD REPLY • link written 2.1 years ago by y.hoogstrate • 460

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