/external_service_types/pacific_biosciences_smrt_portal.xml

<external_service id="pacific_biosciences_smrt_portal" name="Pacific Biosciences SMRT Portal" version="1.1.0">
    <description></description>
    <version>1</version>
    <data_transfer_settings>
        <data_transfer protocol='http' automatic_transfer='True' />
    </data_transfer_settings>
    <run_details>
        <results>
            <dataset name="dataset2_name" datatype="dataset2_datatype"
                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/filtered_subreads.fa" />
            <dataset name="dataset3_name" datatype="dataset3_datatype"
                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/aligned_reads.bam" />
            <dataset name="dataset4_name" datatype="dataset4_datatype"
                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/alignment_summary.gff" />
            <dataset name="dataset5_name" datatype="dataset5_datatype"
                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/coverage.bed" />
            <dataset name="dataset6_name" datatype="dataset6_datatype"
                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/variants.bed" />
            <dataset name="dataset7_name" datatype="dataset7_datatype"
                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/variants.gff.gz" />
        </results>
    </run_details>
    <form type="external_service" name="Pacific Biosciences SMRT Portal Form" description="">
        <fields>
            <field name="host" type="text" label="Hostname or IP address" description="" value="192.168.56.101" required="True" />
            <field name="user_name" type="text" label="User name" description="User name to log into the sequencer." value="administrator" required="True" />
            <field name="password" type="password" label="Password" description="" value="galaxy" required="True" />
            <field name="data_location" type="text" label="Data directory" description="" value="" required="False" />
            
            <field name="dataset2_name" type="text" label="Filtered reads" description="" value="Filtered reads" required="True" />
            <field name="dataset2_datatype" type="text" label="Format" description="" value="fasta" required="True" />
            
            <field name="dataset3_name" type="text" label="Aligned reads bam" description="" value="Aligned reads" required="True" />
            <field name="dataset3_datatype" type="text" label="Format" description="" value="bam" required="True" />
            
            <field name="dataset4_name" type="text" label="Coverage gff" description="" value="Coverage (gff)" required="True" />
            <field name="dataset4_datatype" type="text" label="Format" description="" value="gff" required="True" />
            
            <field name="dataset5_name" type="text" label="Coverage bed" description="" value="Coverage (bed)" required="True" />
            <field name="dataset5_datatype" type="text" label="Format" description="" value="bed" required="True" />
            
            <field name="dataset6_name" type="text" label="Variants bed" description="" value="Variants (bed)" required="True" />
            <field name="dataset6_datatype" type="text" label="Format" description="" value="bed" required="True" />

            <field name="dataset7_name" type="text" label="Variants gff" description="" value="Variants (gff)" required="True" />
            <field name="dataset7_datatype" type="text" label="Format" description="" value="gff" required="True" />
        </fields>
    </form>
    
    <actions>
        <param name="api_url" type="template">http://${fields.host}/smrtportal/api</param>
        <param name="web_url" type="template">http://${fields.host}/smrtportal/#</param>
        <section name="jobs" label="Job Service">
        
            <param name="jobs_url" type="template">${api_url}/Jobs</param>
            <param name="monitor_jobs_url" type="template">${web_url}/MonitorJobs</param>
            <!--
            <action type="web_api" name="jobs_list" label="List Jobs" description="">
                <request target="galaxy_main" method="post">
                    <url>${jobs.jobs_url}</url>
                </request>
                <result_handler type="jquery_grid"></result_handler>
            </action>
            -->
            <conditional name="job_sample" label="Sample to Job Service" ref="item">
                <when type="item_type" name="sample" value="sample">
                    <param name="secondary_analysis_job_id" type="template">${item.run_details.run.info.content.get( 'secondary_analysis_job_id' )}</param>
                    <conditional name="valid_job_sample" ref="jobs.job_sample.sample.secondary_analysis_job_id">
                        <when type="boolean" name="valid">
                            <param name="job_sample_url" type="template">${jobs.jobs_url}/${jobs.job_sample.sample.secondary_analysis_job_id}</param>
                            <param name="monitor_job_url" type="template">${jobs.monitor_jobs_url}/DetailsOfJob/${jobs.job_sample.sample.secondary_analysis_job_id}</param>

                            <action type="web" name="monitor_job" label="View Job in SMRT Portal" description="">
                                <request target="_blank" method="get">
                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.monitor_job_url}</url>
                                </request>
                            </action>

                            <action type="web_api" name="job_status" label="Job status" description="">
                                <request target="galaxy_main" method="post">
                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Status</url>
                                </request>
                                <result_handler type="json_display"></result_handler>
                            </action>

                            <action type="web_api" name="job_history" label="Job history" description="">
                                <request target="galaxy_main" method="post">
                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/History</url>
                                </request>
                                <result_handler type="jquery_grid"></result_handler>
                            </action>
                            
                            <action type="web_api" name="job_log" label="Job log" description="">
                                <request target="galaxy_main" method="post">
                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Log</url>
                                </request>
                                <result_handler type="display"></result_handler>
                            </action>
                            
                            <action type="web_api" name="job_contents" label="Job contents" description="">
                                <request target="galaxy_main" method="post">
                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Contents</url>
                                </request>
                                <result_handler type="json_display"></result_handler>
                            </action>
                            <!--
                            <action type="web_api" name="job_protocol" label="Job protocol" description="">
                                <request target="galaxy_main" method="post">
                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Protocol</url>
                                </request>
                                <result_handler type="display"></result_handler>
                            </action>
                            -->
                            <action type="web_api" name="job_inputs" label="Job inputs" description="">
                                <request target="galaxy_main" method="post">
                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Inputs</url>
                                </request>
                                <result_handler type="jquery_grid"></result_handler>
                            </action>
                            
                            <action type="template" name="job_smrt_view" label="Job SMRT View" description="">
                                <template>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Contents/vis.jnlp</template>
                                <result_handler type="web_redirect"></result_handler>
                            </action>

                        </when>
                    </conditional>
                </when>
            </conditional>
            
        </section>
    </actions>
    
</external_service>