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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