diff haplotype_caller.xml @ 14:d73c92a7b0ea draft

Remove unneeded params

--- a/haplotype_caller.xml	Thu Nov 08 11:50:01 2012 -0600
+++ b/haplotype_caller.xml	Thu Nov 08 13:09:56 2012 -0600
@@ -25,7 +25,6 @@
     #if str($input_recal) != 'None':
         --BQSR "${input_recal}"
     #end if
-    --disable_bam_indexing
    '
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
@@ -71,7 +70,6 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
-        ${gatk_param_type.disable_experimental_low_memory_sharding}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -406,92 +404,10 @@
           </conditional>
         </repeat>
         
-        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
         
       </when>
     </conditional>
-    
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
-
-        <conditional name="default_read_group_type">
-          <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
-            <option value="default" selected="True">Don't Set</option>
-            <option value="set">Set</option>
-          </param>
-          <when value="default">
-            <!-- do nothing here -->
-          </when>
-          <when value="set">
-            <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
-          </when>
-        </conditional>
-        <param name="default_platform" type="select" label="Set default Platform" help="--default_platform">
-          <option value="default" selected="True">Don't Set</option>
-          <option value="illumina">illumina</option>
-          <option value="454">454</option>
-          <option value="solid">solid</option>
-        </param>
-        <conditional name="force_read_group_type">
-          <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group">
-            <option value="default" selected="True">Don't Force</option>
-            <option value="set">Force</option>
-          </param>
-          <when value="default">
-            <!-- do nothing here -->
-          </when>
-          <when value="set">
-            <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
-          </when>
-        </conditional>
-        <param name="force_platform" type="select" label="Force Platform" help="--force_platform">
-          <option value="default" selected="True">Don't Force</option>
-          <option value="illumina">illumina</option>
-          <option value="454">454</option>
-          <option value="solid">solid</option>
-        </param>
-        <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/>
-        <conditional name="solid_options_type">
-          <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
-            <option value="default" selected="True">Don't Set</option>
-            <option value="set">Set</option>
-          </param>
-          <when value="default">
-            <!-- do nothing here -->
-          </when>
-          <when value="set">
-            <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &amp;lt;solid_recal_mode&amp;gt;">
-              <option value="default" selected="True">Don't set</option>
-              <option value="DO_NOTHING">DO_NOTHING</option>
-              <option value="SET_Q_ZERO">SET_Q_ZERO</option>
-              <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
-              <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
-            </param>
-            <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &amp;lt;solid_nocall_strategy&amp;gt;">
-              <option value="default" selected="True">Don't set</option>
-              <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
-              <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
-              <option value="PURGE_READ">PURGE_READ</option>
-            </param>
-          </when>
-        </conditional>
-        <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
-        <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="--window_size_nqs"/>
-        <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
-        <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated" help="-pQ,--preserve_qscores_less_than &amp;lt;preserve_qscores_less_than&amp;gt;"/>
-        <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &amp;lt;smoothing&amp;gt;"/>
-        <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &amp;lt;max_quality_score&amp;gt;"/>
-        <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/>
-      </when>
-    </conditional>
 
     <conditional name="analysis_param_type">
       <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
@@ -578,8 +494,8 @@
   <help>
 **What it does**
 
-HaplotypeCaller
-Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region.
+**HaplotypeCaller**
+calls SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region.
 Haplotypes are evaluated using an affine gap penalty Pair HMM.
 
 For more information on using read based compression in the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_haplotypecaller_HaplotypeCaller.html&gt;`_.
@@ -592,7 +508,7 @@
 
 **Inputs**
 
-GenomeAnalysisTK: PrintReads accepts an aligned BAM files.
+GenomeAnalysisTK: PrintReads accepts aligned BAM files.
 
 
 **Outputs**
@@ -606,26 +522,6 @@
 
 **Settings**::
 
- default_read_group             If a read has no read group then default to the provided String.
- default_platform               If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.
- force_read_group               If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.
- force_platform                 If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.
- window_size_nqs                The window size used by MinimumNQSCovariate for its calculation
- homopolymer_nback              The number of previous bases to look at in HomopolymerCovariate
- exception_if_no_tile           If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1
- solid_recal_mode               How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS)
- solid_nocall_strategy          Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ)
- recal_file                     Filename for the input covariates table recalibration .csv file
- out                            The output BAM file
- bam_compression                Compression level to use for writing BAM files
- disable_bam_indexing           Turn off on-the-fly creation of indices for output BAM files.
- simplifyBAM                    If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier
- preserve_qscores_less_than     Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below &lt; 5, since base callers use these values to indicate random or bad bases
- smoothing                      Number of imaginary counts to add to each bin bin order to smooth out bins with few data points, default=1
- max_quality_score              The integer value at which to cap the quality scores, default=50
- doNotWriteOriginalQuals        If true, we will not write the original quality (OQ) tag for each read
-
-*HaplotypeCaller specific arguments*::
  activeRegionIn              Use this interval list file as the active regions to process
  activeRegionOut             Output the active region to this interval list file
  alleles                     The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES