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comparison base_recalibrator.xml @ 2:8bcc13094767 draft

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author iuc
date Sat, 18 Jan 2014 07:21:33 -0500
parents 340633249b3d
children f244b8209eb8
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1:f760c0de8e3a 2:8bcc13094767
15 @JAR_PATH@ 15 @JAR_PATH@
16 -T "BaseRecalibrator" 16 -T "BaseRecalibrator"
17 \$GATK2_SITE_OPTIONS 17 \$GATK2_SITE_OPTIONS
18 18
19 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975 19 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
20 --num_cpu_threads_per_data_thread 8 20 --num_cpu_threads_per_data_thread \${GALAXY_SLOTS:-8}
21 21
22 @THREADS@
23 ## we set non standards at every run and the user can choose which ones are preferred 22 ## we set non standards at every run and the user can choose which ones are preferred
24 ## in our select box both standard options (ContextCovariate, CycleCovariate) are selected by default 23 ## in our select box both standard options (ContextCovariate, CycleCovariate) are selected by default
25 --no_standard_covs 24 --no_standard_covs
26 25
27 #if $reference_source.reference_source_selector != "history": 26 #if $reference_source.reference_source_selector != "history":
109 <filter type="data_meta" key="dbkey" ref="input_bam" /> 108 <filter type="data_meta" key="dbkey" ref="input_bam" />
110 </options> 109 </options>
111 </param> 110 </param>
112 </when> 111 </when>
113 </conditional> 112 </conditional>
114 <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" > 113 <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="The input covariates table file which enables on-the-fly base quality score recalibration. Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool. Please be aware that one should only run recalibration with the covariates file created on the same input bam(s) (-BQSR,--BQSR &amp;lt;recal_file&amp;gt;)" />
115 <help>The input covariates table file which enables on-the-fly base quality score recalibration.
116 Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool.
117 Please be aware that one should only run recalibration with the covariates file created on the same input bam(s).
118 </help>
119 </param>
120 114
121 <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" > 115 <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
122 <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? --> 116 <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
123 <option value="ContextCovariate" selected="true"/> 117 <option value="ContextCovariate" selected="true"/>
124 <option value="CycleCovariate" selected="true"/> 118 <option value="CycleCovariate" selected="true"/>