<?xml version="1.0" encoding="UTF-8"?>

<commandSetRoot xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation='commandSet.xsd'>
    <commandSet type="serial">
        <state>incomplete</state>
        <name>bwa Iterator workflow</name>
        <!--Processing-->
        <command>
            <type>RunUnixCommand</type>
            <name>create output directory</name>
            <state>incomplete</state>
            <executable>mkdir</executable>
            <arg>-p -m 777 $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;</arg>
        </command>
        <command>
            <type>RunUnixCommand</type>
            <name>create temp directory</name>
            <state>incomplete</state>
            <executable>mkdir</executable>
            <arg>-p -m 777 $;TMP_DIR$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;</arg>
        </command>
        <command>
            <type>RunUnixCommand</type>
            <name>BWA Execution</name>
            <state>incomplete</state>
            <executable>$;BIN_DIR$;/lgt_bwa</executable>            
            <param>
            <key>--input_dir</key>
            <value>$;I_DIR$;</value>
            </param>
            <param>
            <key>--input_base</key>
            <value>$;I_FILE_BASE$;</value>
            </param>
            <param>
            <key>--ref_file_list</key>
            <value>$;REF_FILE_LIST1$;</value>
            </param>
            <param>
            <key>--ref_file</key>
            <value>$;REF_FILE1$;</value>
            </param>
            <param>
            <key>--output_dir</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/</value>
            </param>  
            <param>
            <key>--mistmatch</key>
            <value>$;MISMATCH_PENALTY$;</value>
            </param>  
            <param>
            <key>--max_gaps</key>
            <value>$;MAX_GAP_OPENS$;</value>
            </param>
            <param>
            <key>--max_gap_extensions</key>
            <value>$;MAX_GAP_EXTNS$;</value>
            </param>
            <param>
            <key>--open_gap_penalty</key>
            <value>$;GAP_OPEN_PENALTY$;</value>
            </param> 
            <param>    
            <key>--extend_gap_penalty</key>
            <value>$;GAP_EXTN_PENALTY$;</value>
            </param>     
            <param>
            <key>--threads</key>
            <value>$;MAX_THREADS$;</value>
            </param>     
            <param>
            <key>--use_bwasw</key>
            <value>$;BWASW$;</value>
            </param> 
            <param>
            <key>--num_aligns</key>
            <value>$;MAX_ALIGN$;</value>
            </param> 
            <param>
            <key>--bwa_path</key>
            <value>$;BWA_EXEC$;</value>
            </param>
            <param>
            <key>--cleanup_sai</key>
            <value>$;CLEANUP$;</value>
            </param>
            <param>
            <key>stdout</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.bwa_align_exec.ref1.stdout</value>
            </param>
            <param>
            <key>stderr</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.bwa_align_exec.ref1.stderr</value>
            </param>
        </command>
        <command>
            <type>RunUnixCommand</type>
            <name>BWA Execution</name>
            <state>incomplete</state>
            <executable>$;BIN_DIR$;/lgt_bwa</executable>            
            <param>
            <key>--input_dir</key>
            <value>$;I_DIR$;</value>
            </param>
            <param>
            <key>--input_base</key>
            <value>$;I_FILE_BASE$;</value>
            </param>
            <param>
            <key>--ref_file_list</key>
            <value>$;REF_FILE_LIST2$;</value>
            </param>
            <param>
            <key>--ref_file</key>
            <value>$;REF_FILE2$;</value>
            </param>
            <param>
            <key>--output_dir</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/</value>
            </param>         
            <param>
            <key>--mistmatch</key>
            <value>$;MISMATCH_PENALTY$;</value>
            </param>  
            <param>
            <key>--max_gaps</key>
            <value>$;MAX_GAP_OPENS$;</value>
            </param>  
            <param>
            <key>--max_gap_extensions</key>
            <value>$;MAX_GAP_EXTNS$;</value>
            </param>     
            <param>
            <key>--open_gap_penalty</key>
            <value>$;GAP_OPEN_PENALTY$;</value>
            </param>     
            <param>
            <key>--extend_gap_penalty</key>
            <value>$;GAP_EXTN_PENALTY$;</value>
            </param>     
            <param>
            <key>--threads</key>
            <value>$;MAX_THREADS$;</value>
            </param>     
            <param>
            <key>--use_bwasw</key>
            <value>$;BWASW$;</value>
            </param> 
            <param>
            <key>--num_aligns</key>
            <value>$;MAX_ALIGN$;</value>
            </param> 
            <param>
            <key>--bwa_path</key>
            <value>$;BWA_EXEC$;</value>
            </param>
            <param>
            <key>--cleanup_sai</key>
            <value>$;CLEANUP$;</value>
            </param>
            <param>
            <key>stdout</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.bwa_align_exec.ref2.stdout</value>
            </param>
            <param>
            <key>stderr</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.bwa_align_exec.ref2.stderr</value>
            </param>
        </command>
        <command>
            <type>RunUnixCommand</type>
            <name>POST PROCESSING</name>
            <state>incomplete</state>
            <executable>$;BIN_DIR$;/lgt_bwa_post_process</executable>            
            <param>
            <key>stdout</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.postprocess_exec.stdout</value>
            </param>
            <param>
            <key>stderr</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.postprocess_exec.stderr</value>
            </param>
            <param>
            <key>--input</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;</value>
            </param>
            <param>
            <key>--ref1</key>
            <value>$;REF_FILE1$;</value>
            </param>
            <param>
            <key>--ref2</key>
            <value>$;REF_FILE2$;</value>
            </param>
            <param>
            <key>--ref_list1</key>
            <value>$;REF_FILE_LIST1$;</value>
            </param>
            <param>
            <key>--ref_list2</key>
            <value>$;REF_FILE_LIST2$;</value>
            </param>
        </command>
        <command>
            <type>RunUnixCommand</type>
            <name>ZIP FILES</name>
            <state>incomplete</state>
            <executable>$;BIN_DIR$;/lgt_bwa_zip.sh</executable>            
            <param>
            <key>stdout</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.zip_files_exec.stdout</value>
            </param>
            <param>
            <key>stderr</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.zip_files_exec.stderr</value>
            </param>
            <arg>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;</arg>
        </command>
        <command>
            <type>RunUnixCommand</type>
            <name>REMOVE FASTQ FILES</name>
            <state>incomplete</state>
            <executable>$;BIN_DIR$;/lgt_bwa_rm.sh</executable>            
            <param>
            <key>stdout</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.remove_fastq_exec.stdout</value>
            </param>
            <param>
            <key>stderr</key>
            <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.remove_fastq_exec.stderr</value>
            </param>
	    <arg>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;</arg>
        </command>
    </commandSet>
</commandSetRoot>