--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/gatk/count_covariates.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,431 @@
+<tool id="gatk_count_covariates" name="Count Covariates" version="0.0.1">
+  <description>on BAM files</description>
+  <command interpreter="python">gatk_wrapper.py
+   --stdout "${output_log}"
+   -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+   -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+   -p 'java 
+    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
+    -T "CountCovariates"
+    --num_threads 4 ##hard coded, for now
+    -et "NO_ET" ##ET no phone home
+    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
+    #if $reference_source.reference_source_selector != "history":
+        -R "${reference_source.ref_file.fields.path}"
+    #end if
+    --recal_file "${output_recal}"
+    ${standard_covs}
+    #if $covariates.value:
+        #for $cov in $covariates.value:
+            -cov "${cov}"
+        #end for
+    #end if
+   '
+    
+    #set $snp_dataset_provided = False
+    #if str( $input_dbsnp_rod ) != "None":
+        -d "-D" "${input_dbsnp_rod}" "${input_dbsnp_rod.ext}" "dbsnp_rod"
+        #set $snp_dataset_provided = True
+    #end if
+    #set $rod_binding_names = dict()
+    #for $rod_binding in $rod_bind:
+        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
+            #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
+        #else
+            #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
+        #end if
+        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'snps':
+            #set $snp_dataset_provided = True
+        #end if
+        #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
+        -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
+            -p '--rodToIntervalTrackName "${rod_bind_name}"'
+        #end if
+    #end for
+    
+    ##start standard gatk options
+    #if $gatk_param_type.gatk_param_type_selector == "advanced":
+        #for $sample_metadata in $gatk_param_type.sample_metadata:
+            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #end for
+        #for $read_filter in $gatk_param_type.read_filter:
+            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
+            ###raise Exception( str( dir( $read_filter ) ) )
+            #for $name, $param in $read_filter.read_filter_type.iteritems():
+                #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
+                    --${name} "${param}"
+                #end if
+            #end for
+            '
+        #end for
+        #if str( $gatk_param_type.input_intervals ) != "None":
+            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
+        #end if
+        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
+            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
+        #end if
+        
+        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
+        #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
+            -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
+        #end if
+        -p '
+        --baq "${gatk_param_type.baq}"
+        --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
+        ${gatk_param_type.use_original_qualities}
+        --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
+        --validation_strictness "${gatk_param_type.validation_strictness}"
+        --interval_merging "${gatk_param_type.interval_merging}"
+        '
+        #if str( $gatk_param_type.read_group_black_list ) != "None":
+            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
+        #end if
+    #end if
+    #if str( $reference_source.reference_source_selector ) == "history":
+        -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
+    #end if
+    ##end standard gatk options
+    
+    ##start analysis specific options
+    #if $analysis_param_type.analysis_param_type_selector == "advanced":
+        -p '
+        #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
+            --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
+        #end if
+        #if str( $analysis_param_type.default_platform ) != "default":
+            --default_platform "${analysis_param_type.default_platform}"
+        #end if
+        #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
+            --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
+        #end if
+        #if str( $analysis_param_type.force_platform ) != "default":
+            --force_platform "${analysis_param_type.force_platform}"
+        #end if
+        ${analysis_param_type.exception_if_no_tile}
+        #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
+            #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
+                --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}" 
+            #end if
+            #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
+                --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}" 
+            #end if
+        #end if
+        --window_size_nqs "${analysis_param_type.window_size_nqs}"
+        --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
+        '
+    #end if
+    #if not $snp_dataset_provided:
+        -p '--run_without_dbsnp_potentially_ruining_quality'
+    #end if
+  </command>
+  <inputs>
+    <conditional name="reference_source">
+      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
+        <option value="cached">Locally cached</option>
+        <option value="history">History</option>
+      </param>
+      <when value="cached">
+        <param name="input_bam" type="data" format="bam" label="BAM file">
+          <validator type="unspecified_build" />
+          <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+        </param>
+        <param name="ref_file" type="select" label="Using reference genome">
+          <options from_data_table="picard_indexes">
+            <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
+          </options>
+        </param>
+      </when>
+      <when value="history"> <!-- FIX ME!!!! -->
+        <param name="input_bam" type="data" format="bam" label="BAM file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+      </when>
+    </conditional>
+    <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" />
+    <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" >
+      <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
+      <option value="ReadGroupCovariate" />
+      <option value="QualityScoreCovariate" />
+      <option value="CycleCovariate" />
+      <option value="DinucCovariate" />
+      <!-- covariates below were pull from source code, since the list option doesn't seem to work (when tried) -->
+      <option value="HomopolymerCovariate" />
+      <option value="MappingQualityCovariate" />
+      <option value="MinimumNQSCovariate" />
+      <option value="PositionCovariate" />
+      <option value="PrimerRoundCovariate" />
+      <option value="TileCovariate" />
+    </param>
+    <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" />
+    <repeat name="rod_bind" title="Binding for reference-ordered data">
+        <conditional name="rod_bind_type">
+	      <param name="rod_bind_type_selector" type="select" label="Binding Type">
+	        <option value="snps" selected="True">SNPs</option>
+	        <option value="indels">INDELs</option>
+	        <option value="mask">Mask</option>
+	        <option value="custom">Custom</option>
+	      </param>
+          <when value="snps">
+              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+          </when>
+          <when value="indels">
+              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+          </when>
+          <when value="custom">
+              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
+              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+          </when>
+        </conditional>
+    </repeat>
+    
+    <conditional name="gatk_param_type">
+      <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
+        <option value="basic" selected="True">Basic</option>
+        <option value="advanced">Advanced</option>
+      </param>
+      <when value="basic">
+        <!-- Do nothing here -->
+      </when>
+      <when value="advanced">
+        <repeat name="sample_metadata" title="Sample Metadata">
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+        </repeat>
+        <repeat name="read_filter" title="Read Filter">
+            <conditional name="read_filter_type">
+		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
+		        <option value="MaxReadLength" selected="True">MaxReadLength</option>
+		        <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
+		      </param>
+	          <when value="ZeroMappingQualityRead">
+	              <!-- no extra options -->
+	          </when>
+	          <when value="MaxReadLength">
+	              <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
+	          </when>
+            </conditional>
+        </repeat>
+        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
+        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+          <option value="UNION" selected="True">UNION</option>
+          <option value="INTERSECTION">INTERSECTION</option>
+        </param>
+        <conditional name="downsampling_type">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+            <option value="NONE" selected="True">NONE</option>
+            <option value="ALL_READS">ALL_READS</option>
+            <option value="BY_SAMPLE">BY_SAMPLE</option>
+          </param>
+          <when value="NONE">
+	          <!-- no more options here -->
+	      </when>
+          <when value="ALL_READS">
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when>
+          <when value="BY_SAMPLE">
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when>
+        </conditional>
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
+          <option value="OFF" selected="True">OFF</option>
+          <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
+          <option value="RECALCULATE">RECALCULATE</option>
+        </param>
+        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="LENIENT">LENIENT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
+        <param name="interval_merging" type="select" label="Interval merging rule">
+          <option value="ALL" selected="True">ALL</option>
+          <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
+        </param>
+        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+      </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">
+            <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">
+          <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">
+            <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">
+          <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"/>
+        <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">
+              <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">
+              <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="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/>
+        <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" />
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="csv" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" />
+    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+  </outputs>
+  <tests>
+      <test>
+          <param name="reference_source_selector" value="history" />
+          <param name="ref_file" value="phiX.fasta" ftype="fasta" />
+          <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
+          <param name="input_dbsnp_rod"  />
+          <param name="rod_bind_type_selector" value="snps" />
+          <param name="rodToIntervalTrackName" />
+          <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
+          <param name="standard_covs" value="True" />
+          <param name="covariates" value="ReadGroupCovariate,HomopolymerCovariate,MinimumNQSCovariate,PositionCovariate" />
+          <param name="gatk_param_type_selector" value="basic" />
+          <param name="analysis_param_type_selector" value="basic" />
+          <output name="output_recal" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" /> 
+          <output name="output_log" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains" compare="contains" />
+      </test>
+  </tests>
+  <help>
+.. class:: warningmark
+
+"This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation."
+However, if you do not provide this file, the '--run_without_dbsnp_potentially_ruining_quality' flag will be automatically used, and the command will be allowed to run.
+  
+**What it does**
+
+     This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal 
+     operating only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors 
+     and indicative of poor base quality. This walker generates tables based on various user-specified covariates (such 
+     as read group, reported quality score, cycle, and dinucleotide) Since there is a large amount of data one can then 
+     calculate an empirical probability of error given the particular covariates seen at this site, where p(error) = num 
+     mismatches / num observations The output file is a CSV list of (the several covariate values, num observations, num 
+     mismatches, empirical quality score) The first non-comment line of the output file gives the name of the covariates 
+     that were used for this calculation.  Note: ReadGroupCovariate and QualityScoreCovariate are required covariates 
+     and will be added for the user regardless of whether or not they were specified Note: This walker is designed to be 
+     used in conjunction with TableRecalibrationWalker.
+
+
+------
+
+Please cite the website "http://addlink.here" as well as:
+
+Add citation here 2011.
+
+------
+
+**Input formats**
+
+GenomeAnalysisTK: CountCovariates accepts an aligned BAM input file.
+
+------
+
+**Outputs**
+
+The output is in CSV format, see http://addlink.here for more details.
+
+-------
+
+**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 CSV file
+ recal_file                                                     Filename for the outputted covariates table recalibration file
+ standard_covs                                                                Use the standard set of covariates in addition to the ones listed using the -cov argument
+ run_without_dbsnp_potentially_ruining_quality   If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only.
+
+  </help>
+</tool>