samtools-sort.json

{"available":true,
 "checkpointable":false,
 "defaultMemoryPerNode":32,
 "defaultProcessorsPerNode":16,
 "defaultMaxRunTime":"08:00:00",
 "defaultNodeCount":1,
 "defaultQueue":"serial",
 "deploymentPath":"vaughn/applications/samtools-0.1.19/stampede",
 "deploymentSystem":"data.iplantcollaborative.org",
 "executionSystem":"stampede-04012014-1718-vaughn",
 "executionType":"HPC",
 "helpURI":"http://samtools.sourceforge.net/samtools.shtml",
 "label": "SAMtools sort",
 "longDescription":"",
 "modules":[],
 "name":"samtools-sort",
 "ontology":["http://sswapmeet.sswap.info/agave/apps/Application"],
 "parallelism":"SERIAL",
 "shortDescription":"Sort a BAM file by name or coordinate",
 "tags":["aligner","NGS","SAM"],
 "templatePath":"sort.template",
 "testPath":"test-sort.sh",
 "version":"0.1.19",
 "inputs":[
    {"id":"inputBam",
     "value":
        {"default":"input.bam",
         "order":0,
         "required":true,
         "validator":"([^\\s]+(\\.(?i)(bam))$)",
         "visible":true},
     "semantics":
        {"ontology":["http://sswapmeet.sswap.info/mime/application/X-bam"],
         "minCardinality":1,
         "fileTypes":["raw-0"]},
     "details":
        {"description":"",
         "label":"The BAM file to sort",
         "argument":null,
         "showArgument":false}}],
 "parameters":[
    {"id":"maxMemSort",
     "value":
        {"default":500000000,
         "order":1,
         "required":true,
         "type":"number",
         "validator":"",
         "visible":true},
     "semantics":
        {"ontology":["xs:integer"]},
     "details":
        {"description":null,
         "label":"Maxiumum memory in bytes, used for sorting",
         "argument":"-m ",
         "showArgument":false}},
    {"id":"nameSort",
     "value":
        {"default":false,
         "order":1,
         "required":false,
         "type":"bool",
         "validator":"",
         "visible":true},
     "semantics":
        {"ontology":["xs:boolean"]},
     "details":
        {"description":null,
         "label":"Sort by name rather than coordinate",
         "argument":"-n ",
         "showArgument":false}}],
 "outputs":[
    {"id":"bam",
     "value":
        {"default":"sorted.bam",
         "order":0,
         "required":false,
         "validator":"",
         "visible":true},
     "semantics":
        {"ontology":["http://sswapmeet.sswap.info/mime/application/X-bam"],
         "minCardinality":1,
         "fileTypes":["raw-0"]},
     "details":
        {"description":"",
         "label":"Sorted BAM file",
         "argument":null,
         "showArgument":false}}]}