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comparison print_reads.xml @ 4:f244b8209eb8 draft

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bug fix release
author iuc
date Mon, 25 Aug 2014 17:43:11 -0400
parents 8bcc13094767
children 35c00763cb5c
comparison
equal deleted inserted replaced
3:2553f84b8174 4:f244b8209eb8
1 <tool id="gatk2_print_reads" name="Print Reads" version="0.0.7"> 1 <tool id="gatk2_print_reads" name="Print Reads" version="@VERSION@.0">
2 <description>on BAM files</description> 2 <description>on BAM files</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>gatk2_macros.xml</import> 5 <import>gatk2_macros.xml</import>
6 </macros> 6 </macros>
29 #end if 29 #end if
30 --disable_bam_indexing 30 --disable_bam_indexing
31 ' 31 '
32 32
33 #include source=$standard_gatk_options# 33 #include source=$standard_gatk_options#
34
35 #if str( $reference_source.reference_source_selector ) == "history":
36 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
37 #end if
38 ##end standard gatk options
39 34
40 ##start analysis specific options 35 ##start analysis specific options
41 #if $analysis_param_type.analysis_param_type_selector == "advanced": 36 #if $analysis_param_type.analysis_param_type_selector == "advanced":
42 -p ' 37 -p '
43 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set": 38 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
200 <help> 195 <help>
201 **What it does** 196 **What it does**
202 197
203 This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads. Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with CovariateCounterWalker. 198 This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads. Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with CovariateCounterWalker.
204 199
205 For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_PrintReads.html&gt;`_. 200 For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_readutils_PrintReads.html&gt;`_.
206 201
207 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_. 202 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
208 203
209 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_. 204 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
210 205
245 max_quality_score The integer value at which to cap the quality scores, default=50 240 max_quality_score The integer value at which to cap the quality scores, default=50
246 doNotWriteOriginalQuals If true, we will not write the original quality (OQ) tag for each read 241 doNotWriteOriginalQuals If true, we will not write the original quality (OQ) tag for each read
247 242
248 @CITATION_SECTION@ 243 @CITATION_SECTION@
249 </help> 244 </help>
245 <expand macro="citations" />
250 </tool> 246 </tool>