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> ~~~~