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/external_service_types/pacific_biosciences_smrt_portal.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 134 lines | 101 code | 17 blank | 16 comment | 0 complexity | ad76d010a2fd135b1c7ffcc04e3ac226 MD5 | raw file
  1<external_service id="pacific_biosciences_smrt_portal" name="Pacific Biosciences SMRT Portal" version="1.1.0">
  2    <description></description>
  3    <version>1</version>
  4    <data_transfer_settings>
  5        <data_transfer protocol='http' automatic_transfer='True' />
  6    </data_transfer_settings>
  7    <run_details>
  8        <results>
  9            <dataset name="dataset2_name" datatype="dataset2_datatype"
 10                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/filtered_subreads.fa" />
 11            <dataset name="dataset3_name" datatype="dataset3_datatype"
 12                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/aligned_reads.bam" />
 13            <dataset name="dataset4_name" datatype="dataset4_datatype"
 14                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/alignment_summary.gff" />
 15            <dataset name="dataset5_name" datatype="dataset5_datatype"
 16                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/coverage.bed" />
 17            <dataset name="dataset6_name" datatype="dataset6_datatype"
 18                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/variants.bed" />
 19            <dataset name="dataset7_name" datatype="dataset7_datatype"
 20                     url="http://${host}/smrtportal/api/Jobs/${secondary_analysis_job_id}/Contents/data/variants.gff.gz" />
 21        </results>
 22    </run_details>
 23    <form type="external_service" name="Pacific Biosciences SMRT Portal Form" description="">
 24        <fields>
 25            <field name="host" type="text" label="Hostname or IP address" description="" value="192.168.56.101" required="True" />
 26            <field name="user_name" type="text" label="User name" description="User name to log into the sequencer." value="administrator" required="True" />
 27            <field name="password" type="password" label="Password" description="" value="galaxy" required="True" />
 28            <field name="data_location" type="text" label="Data directory" description="" value="" required="False" />
 29            
 30            <field name="dataset2_name" type="text" label="Filtered reads" description="" value="Filtered reads" required="True" />
 31            <field name="dataset2_datatype" type="text" label="Format" description="" value="fasta" required="True" />
 32            
 33            <field name="dataset3_name" type="text" label="Aligned reads bam" description="" value="Aligned reads" required="True" />
 34            <field name="dataset3_datatype" type="text" label="Format" description="" value="bam" required="True" />
 35            
 36            <field name="dataset4_name" type="text" label="Coverage gff" description="" value="Coverage (gff)" required="True" />
 37            <field name="dataset4_datatype" type="text" label="Format" description="" value="gff" required="True" />
 38            
 39            <field name="dataset5_name" type="text" label="Coverage bed" description="" value="Coverage (bed)" required="True" />
 40            <field name="dataset5_datatype" type="text" label="Format" description="" value="bed" required="True" />
 41            
 42            <field name="dataset6_name" type="text" label="Variants bed" description="" value="Variants (bed)" required="True" />
 43            <field name="dataset6_datatype" type="text" label="Format" description="" value="bed" required="True" />
 44
 45            <field name="dataset7_name" type="text" label="Variants gff" description="" value="Variants (gff)" required="True" />
 46            <field name="dataset7_datatype" type="text" label="Format" description="" value="gff" required="True" />
 47        </fields>
 48    </form>
 49    
 50    <actions>
 51        <param name="api_url" type="template">http://${fields.host}/smrtportal/api</param>
 52        <param name="web_url" type="template">http://${fields.host}/smrtportal/#</param>
 53        <section name="jobs" label="Job Service">
 54        
 55            <param name="jobs_url" type="template">${api_url}/Jobs</param>
 56            <param name="monitor_jobs_url" type="template">${web_url}/MonitorJobs</param>
 57            <!--
 58            <action type="web_api" name="jobs_list" label="List Jobs" description="">
 59                <request target="galaxy_main" method="post">
 60                    <url>${jobs.jobs_url}</url>
 61                </request>
 62                <result_handler type="jquery_grid"></result_handler>
 63            </action>
 64            -->
 65            <conditional name="job_sample" label="Sample to Job Service" ref="item">
 66                <when type="item_type" name="sample" value="sample">
 67                    <param name="secondary_analysis_job_id" type="template">${item.run_details.run.info.content.get( 'secondary_analysis_job_id' )}</param>
 68                    <conditional name="valid_job_sample" ref="jobs.job_sample.sample.secondary_analysis_job_id">
 69                        <when type="boolean" name="valid">
 70                            <param name="job_sample_url" type="template">${jobs.jobs_url}/${jobs.job_sample.sample.secondary_analysis_job_id}</param>
 71                            <param name="monitor_job_url" type="template">${jobs.monitor_jobs_url}/DetailsOfJob/${jobs.job_sample.sample.secondary_analysis_job_id}</param>
 72
 73                            <action type="web" name="monitor_job" label="View Job in SMRT Portal" description="">
 74                                <request target="_blank" method="get">
 75                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.monitor_job_url}</url>
 76                                </request>
 77                            </action>
 78
 79                            <action type="web_api" name="job_status" label="Job status" description="">
 80                                <request target="galaxy_main" method="post">
 81                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Status</url>
 82                                </request>
 83                                <result_handler type="json_display"></result_handler>
 84                            </action>
 85
 86                            <action type="web_api" name="job_history" label="Job history" description="">
 87                                <request target="galaxy_main" method="post">
 88                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/History</url>
 89                                </request>
 90                                <result_handler type="jquery_grid"></result_handler>
 91                            </action>
 92                            
 93                            <action type="web_api" name="job_log" label="Job log" description="">
 94                                <request target="galaxy_main" method="post">
 95                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Log</url>
 96                                </request>
 97                                <result_handler type="display"></result_handler>
 98                            </action>
 99                            
100                            <action type="web_api" name="job_contents" label="Job contents" description="">
101                                <request target="galaxy_main" method="post">
102                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Contents</url>
103                                </request>
104                                <result_handler type="json_display"></result_handler>
105                            </action>
106                            <!--
107                            <action type="web_api" name="job_protocol" label="Job protocol" description="">
108                                <request target="galaxy_main" method="post">
109                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Protocol</url>
110                                </request>
111                                <result_handler type="display"></result_handler>
112                            </action>
113                            -->
114                            <action type="web_api" name="job_inputs" label="Job inputs" description="">
115                                <request target="galaxy_main" method="post">
116                                    <url>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Inputs</url>
117                                </request>
118                                <result_handler type="jquery_grid"></result_handler>
119                            </action>
120                            
121                            <action type="template" name="job_smrt_view" label="Job SMRT View" description="">
122                                <template>${jobs.job_sample.sample.valid_job_sample.valid.job_sample_url}/Contents/vis.jnlp</template>
123                                <result_handler type="web_redirect"></result_handler>
124                            </action>
125
126                        </when>
127                    </conditional>
128                </when>
129            </conditional>
130            
131        </section>
132    </actions>
133    
134</external_service>