trunk/htsworkflow/pipelines/test/testdata/gerald_config_1.0.xml

   1 <RunParameters>
   2 <ChipWideRunParameters>
   3   <ANALYSIS>none</ANALYSIS>
   4   <BAD_LANES></BAD_LANES>
   5   <BAD_LANES></BAD_LANES>
   6   <BAD_LANES></BAD_LANES>
   7   <BAD_TILES></BAD_TILES>
   8   <BIN_DIR>/home/diane/proj/GAPipeline-1.0/Goat/../Gerald/../bin</BIN_DIR>
   9   <CMDPREFIX></CMDPREFIX>
  10   <CONTAM_DIR></CONTAM_DIR>
  11   <CONTAM_FILE></CONTAM_FILE>
  12   <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
  13   <ELAND_MAX_MATCHES></ELAND_MAX_MATCHES>
  14   <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
  15   <ELAND_REPEAT></ELAND_REPEAT>
  16   <ELAND_SEED_LENGTH></ELAND_SEED_LENGTH>
  17   <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
  18   <EMAIL_LIST>diane</EMAIL_LIST>
  19   <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
  20   <EXPT_DIR>/home/diane/gec/090220_HWI-EAS229_0093_30VR0AAXX/Data/C1-37_Firecrest1.9.5_22-02-2009_diane/Bustard1.9.5_22-02-2009_diane</EXPT_DIR>
  21   <EXPT_DIR_ROOT>/home/diane/gec</EXPT_DIR_ROOT>
  22   <FORCE>1</FORCE>
  23   <GENOME_DIR>/home/diane/proj/GAPipeline-1.0/Goat/../Gerald/../../Genomes</GENOME_DIR>
  24   <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
  25   <GROUP_LANES></GROUP_LANES>
  26   <HAMSTER_FLAG>genome</HAMSTER_FLAG>
  27   <HAMSTER_FLAG>genome</HAMSTER_FLAG>
  28   <HAMSTER_FLAG>genome</HAMSTER_FLAG>
  29   <INDEX_BASES></INDEX_BASES>
  30   <NUM_LEADING_DIRS_TO_STRIP>2</NUM_LEADING_DIRS_TO_STRIP>
  31   <ORIG_READ_LENGTHS>37</ORIG_READ_LENGTHS>
  32   <OUT_DIR>/home/diane/gec/090220_HWI-EAS229_0093_30VR0AAXX/Data/C1-37_Firecrest1.9.5_22-02-2009_diane/Bustard1.9.5_22-02-2009_diane/GERALD_22-02-2009_diane</OUT_DIR>
  33   <PAIR_PARAMS></PAIR_PARAMS>
  34   <POST_RUN_COMMAND></POST_RUN_COMMAND>
  35   <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
  36   <PURE_BASES>12</PURE_BASES>
  37   <QCAL_SOURCE></QCAL_SOURCE>
  38   <QCAL_SOURCE1></QCAL_SOURCE1>
  39   <QCAL_SOURCE2></QCAL_SOURCE2>
  40   <QF_PARAMS>'((CHASTITY&gt;=0.6))'</QF_PARAMS>
  41   <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
  42   <QTABLE_PATH></QTABLE_PATH>
  43   <QTABLE_PATH1></QTABLE_PATH1>
  44   <QTABLE_PATH2></QTABLE_PATH2>
  45   <QTABLE_REQUIRED>0</QTABLE_REQUIRED>
  46   <QTABLE_REQUIRED1>0</QTABLE_REQUIRED1>
  47   <QTABLE_REQUIRED2>0</QTABLE_REQUIRED2>
  48   <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
  49   <READ_LENGTH>37</READ_LENGTH>
  50   <READ_LENGTH1>37</READ_LENGTH1>
  51   <READ_LENGTH2>0</READ_LENGTH2>
  52   <SEQUENCE_FORMAT>--scarf</SEQUENCE_FORMAT>
  53   <SEQ_FILE_SUFFIX>_seq.txt</SEQ_FILE_SUFFIX>
  54   <SIG_FILE_SUFFIX_DEPHASED>_sig2.txt</SIG_FILE_SUFFIX_DEPHASED>
  55   <SIG_FILE_SUFFIX_NOT_DEPHASED>_sig.txt</SIG_FILE_SUFFIX_NOT_DEPHASED>
  56   <SMT_FILTER>chastity</SMT_FILTER>
  57   <SMT_RELATION>ge</SMT_RELATION>
  58   <SMT_THRESHOLD>0.6</SMT_THRESHOLD>
  59   <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp</SOFTWARE_VERSION>
  60   <SRF_2ND_CYCLE></SRF_2ND_CYCLE>
  61   <SRF_ARCHIVE_REQUIRED></SRF_ARCHIVE_REQUIRED>
  62   <SRF_CHASTITY>0.6</SRF_CHASTITY>
  63   <SRF_FILE_SUFFIX>_traces.srf</SRF_FILE_SUFFIX>
  64   <SRF_PROCESSED>-P</SRF_PROCESSED>
  65   <SRF_QCAL></SRF_QCAL>
  66   <SRF_RAW>-R</SRF_RAW>
  67   <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
  68   <TILE_ROOT>s</TILE_ROOT>
  69   <TIME_STAMP>Sun Feb 22 21:15:59 2009</TIME_STAMP>
  70   <TOOLS_DIR>/home/diane/proj/GAPipeline-1.0/Goat/../Gerald</TOOLS_DIR>
  71   <USE_BASES>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</USE_BASES>
  72   <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
  73 </ChipWideRunParameters>
  74 <LaneSpecificRunParameters>
  75   <ANALYSIS>
  76     <s_1>eland_extended</s_1>
  77     <s_2>eland_extended</s_2>
  78     <s_3>eland_extended</s_3>
  79     <s_4>eland_extended</s_4>
  80     <s_5>eland_extended</s_5>
  81     <s_6>eland_extended</s_6>
  82     <s_7>eland_extended</s_7>
  83     <s_8>eland_extended</s_8>
  84   </ANALYSIS>
  85   <ELAND_GENOME>
  86     <s_1>/g/mm9</s_1>
  87     <s_2>/g/mm9</s_2>
  88     <s_3>/g/elegans190</s_3>
  89     <s_4>/g/arabidopsis01222004</s_4>
  90     <s_5>/g/mm9</s_5>
  91     <s_6>/g/mm9</s_6>
  92     <s_7>/g/mm9</s_7>
  93     <s_8>/g/mm9</s_8>
  94   </ELAND_GENOME>
  95   <QTABLE_PATH>
  96     <s_1>s_1$(QTABLE_SUFFIX)</s_1>
  97     <s_2>s_2$(QTABLE_SUFFIX)</s_2>
  98     <s_3>s_3$(QTABLE_SUFFIX)</s_3>
  99     <s_4>s_4$(QTABLE_SUFFIX)</s_4>
 100     <s_5>s_5$(QTABLE_SUFFIX)</s_5>
 101     <s_6>s_6$(QTABLE_SUFFIX)</s_6>
 102     <s_7>s_7$(QTABLE_SUFFIX)</s_7>
 103     <s_8>s_8$(QTABLE_SUFFIX)</s_8>
 104   </QTABLE_PATH>
 105   <QTABLE_REQUIRED>
 106     <s_1>1</s_1>
 107     <s_2>1</s_2>
 108     <s_3>1</s_3>
 109     <s_4>1</s_4>
 110     <s_5>1</s_5>
 111     <s_6>1</s_6>
 112     <s_7>1</s_7>
 113     <s_8>1</s_8>
 114   </QTABLE_REQUIRED>
 115   <READ_LENGTH>
 116     <s_1>37</s_1>
 117     <s_2>37</s_2>
 118     <s_3>37</s_3>
 119     <s_4>37</s_4>
 120     <s_5>37</s_5>
 121     <s_6>37</s_6>
 122     <s_7>37</s_7>
 123     <s_8>37</s_8>
 124   </READ_LENGTH>
 125   <SRF_2ND_CYCLE>
 126     <s_1></s_1>
 127     <s_2></s_2>
 128     <s_3></s_3>
 129     <s_4></s_4>
 130     <s_5></s_5>
 131     <s_6></s_6>
 132     <s_7></s_7>
 133     <s_8></s_8>
 134   </SRF_2ND_CYCLE>
 135   <SRF_ARCHIVE_REQUIRED>
 136     <s_1></s_1>
 137     <s_2></s_2>
 138     <s_3></s_3>
 139     <s_4></s_4>
 140     <s_5></s_5>
 141     <s_6></s_6>
 142     <s_7></s_7>
 143     <s_8></s_8>
 144   </SRF_ARCHIVE_REQUIRED>
 145   <USE_BASES>
 146     <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
 147     <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
 148     <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
 149     <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
 150     <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
 151     <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
 152     <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
 153     <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
 154   </USE_BASES>
 155 </LaneSpecificRunParameters>
 156 </RunParameters>