PICARD XSEDE

Used in TBAS, highly restricted options.

tool=PICARD_XSEDE

 PICARD on XSEDE

The commands created by the rest interface are limited.They are:

picard_sortsam
java -Xmx16g -jar /path/picard.jar VALIDATION_STRINGENCY=LENIENT MAX_RECORDS_IN_RAM=7500000 INPUT=/mobyle_share/data/tswv_test_down/A1.sam OUTPUT=/mobyle_share/data/tswv_test_down/A1.bam.sorted.bam SO=coordinate

picard_markduplicates
java -Xmx16g -jar /path/picard.jar MarkDuplicates INPUT=/mobyle_share/data/tswv_test_down/A1.bam.sorted.bam OUTPUT=/mobyle_share/data/tswv_test_down/A1.bam.sorted_marked.bam METRICS_FILE=metrics.txt OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 CREATE_INDEX=true TMP_DIR=/tmp

picard_addreadgroups
java -Xmx16g -jar /path/picard.jar AddOrReplaceReadGroups I=/mobyle_share/data/tswv_test_down/A1.bam.sorted_marked.bam O=/mobyle_share/data/tswv_test_down/A1.bam.sorted_marked_readgroups.bam TMP_DIR=/mobyle_share/data/tswv_test_down/tmp SORT_ORDER=coordinate RGID=A1 RGLB=A1 RGPL=illumina RGPU=A1 RGSM=A1 CREATE_INDEX=True VALIDATION_STRINGENCY=LENIENT

In order to expose all three options, and let any of them be run (except one and three can't be run without nunmber two):
The input file is required. It will be named A1.sam. Even if you don’t run step 1, this file is required.
The other files are added, according to which workflow you choose, 1; 1,2; 1,2,3; 2,3; 3 only.

All these combos should be possible using the run_whatever options. By default all three are activated.

Input files
infile_ = this is the sam file, it is required whatever you do. It will be named A1.sam. If it isn’t needed, it is ignored. There is no way to rename the A1 prefix.
infile2_ = this is the input for a workflow that starts with markduplicates. It will be named A1.bam.sorted.bam
infile3_ = this is the input for a workflow that runs only the third step, Addreadgroups, it will be named A1.bam.sorted_marked.bam.

Visible parameters
runtime_ = float; set the max run time., default=0.25, nmax at 168 h.
run_sortsam_ = switch; default = 1, this runs the first step of the workflow.
run_markduplicates_ = switch; default = 1, this runs the second step of the workflow
run_addreadgroups_ =  swtich; default = 1, this actuates the third step of the workflow.