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