<?xml version="1.0"?>

<craw_conf>
  <!-- Place comments in this file just as this line is placed -->
  <experiment_details>
    <!-- experiment_details is not used for anything at the moment... -->
    <organism>M. musculus</organism>
    <instrument>ltq1</instrument>
    <operator>jasonw</operator>
    <sample_prep>NA</sample_prep>
    <date>03-04-07</date>
    <lc_time>120</lc_time>
    <hplc>Agilent_1100</hplc>
  </experiment_details>
  <experiment_groups>
    <group name='IND'>
      <runs>
      int-01-bs01
      int-02-bs01
      int-03-bs01
      int-04-bs01
      int-05-bs01
      int-06-bs01
      </runs>

      <sqts>
      081605-ecoli-perc-nointra.int.1.sqt
      081605-ecoli-perc-nointra.int.2.sqt
      081605-ecoli-perc-nointra.int.3.sqt
      081605-ecoli-perc-nointra.int.4.sqt
      081605-ecoli-perc-nointra.int.5.sqt
      081605-ecoli-perc-nointra.int.6.sqt
      </sqts>
    </group>
    <group name='UN'>
      <runs>
      un-01-bs01
      un-02-bs01
      un-03-bs01
      un-04-bs01
      un-05-bs01
      un-06-bs01
      </runs>
      <sqts>
      081605-ecoli-perc-nointra.un.1.sqt
      081605-ecoli-perc-nointra.un.2.sqt
      081605-ecoli-perc-nointra.un.3.sqt
      081605-ecoli-perc-nointra.un.4.sqt
      081605-ecoli-perc-nointra.un.5.sqt
      081605-ecoli-perc-nointra.un.6.sqt
      </sqts>
      </group>
      </experiment_groups>



  <actions>
    <global_param name='queue'></global_param>

    <action type='time_interpolate' label='ti'>
      <param name='interval'>0.01</param>
    </action>

    <action type='ms12bins' label='tr' previous='ti'>
      <param name='opts'>--start_trim 25 --stop_trim 100</param>D
    </action>
    
    <action type='ms12bins' label='sg11_w2' previous='tr'>
     <param name='opts'> --sg_order 2 --sg_window 11</param>
    </action>
    
    <action type='align_set' label='aw_ind_3' previous='sg11_w2'>
      <param name='template'>int-03-bs01</param>
      <param name='opts'> --weights 1,2.1,1 --shift_limit 5 </param>
    </action>

    <action type='mean_normalize' label='mn' previous='aw_ind_3'>
     <param name='template'>int-03-bs01</param>
    </action>

    <action type='diffs' label='p005w250_q005' previous='mn'>
      <param name='group1'>UN</param>
      <param name='group2'>IND</param> 
      <param name='ttest_cutoff'>0.005</param>
      <param name='ttest_len_rt'>0.25</param>
      <param name='opts'>  --no_images --perc_q_value=0.005 --max_len_rt=1.1 --start_rt=35.0 --stop_rt=70.0 --uniprot_ids </param>

    </action>


  </actions>
</craw_conf>
