[galaxy-dev] Tool wrapper NotFound error

26 Oct 2016


      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>
~~~~

[galaxy-dev] Tool wrapper NotFound error

evan clark