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 $library.type. Hope this helps and thanks for using Galaxy!
-John
On Wed, Oct 26, 2016 at 11:39 AM, evan clark <eclar...@fau.edu> wrote:
> I have written the below tool wrapper and when running in galaxy I receive
> the error. I am not sure the issue with the wrapper.
> ~~~~
>
> Traceback (most recent call last):
> File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py",
> line 170, in prepare_job
> job_wrapper.prepare()
> File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line
> 897, in prepare
> self.command_line, self.extra_filenames, self.environment_variables =
> tool_evaluator.build()
> File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/tools/evaluation.py",
> line 445, in build
> raise e
> NotFound: cannot find 'library'
>
> ~~~~
>
> ~~~~
> <tool id="miso" name="Miso" version="1.0.0">
>
> <description>Alternative splicing analysis</description>
>
> <version_command>python
> /home/eclark28/galaxy_production/python/lib/python2.7/site-packages/misopy/miso.py
> --version
>
> </version_command>
>
> <command>
>
> <![CDATA[
>
> mkdir -p '${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>
> ~~~~
> ___________________________________________________________
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