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comparison realigner_target_creator.xml @ 0:b83a853a3156

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author devteam
date Tue, 01 Apr 2014 10:49:33 -0400
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1 <tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.4">
2 <description>for use in local realignment</description>
3 <requirements>
4 <requirement type="package" version="1.4">gatk</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement>
6 </requirements>
7 <macros>
8 <import>gatk_macros.xml</import>
9 </macros>
10 <command interpreter="python">gatk_wrapper.py
11 --max_jvm_heap_fraction "1"
12 --stdout "${output_log}"
13 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
14 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
15 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
16 #end if
17 -p 'java
18 -jar "${JAVA_JAR_PATH}/GenomeAnalysisTK.jar"
19 -T "RealignerTargetCreator"
20 -o "${output_interval}"
21 -et "NO_ET" ##ET no phone home
22 --num_threads \${GALAXY_SLOTS:-4}
23 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
24 #if $reference_source.reference_source_selector != "history":
25 -R "${reference_source.ref_file.fields.path}"
26 #end if
27 '
28 #set $rod_binding_names = dict()
29 #for $rod_binding in $rod_bind:
30 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
31 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
32 #else
33 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
34 #end if
35 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
36 -d "-known:${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[$rod_bind_name]}"
37 #end for
38
39 #include source=$standard_gatk_options#
40 ##start analysis specific options
41 #if $analysis_param_type.analysis_param_type_selector == "advanced":
42 -p '
43 --minReadsAtLocus "${analysis_param_type.minReadsAtLocus}"
44 --windowSize "${analysis_param_type.windowSize}"
45 --mismatchFraction "${analysis_param_type.mismatchFraction}"
46 --maxIntervalSize "${analysis_param_type.maxIntervalSize}"
47 '
48 #end if
49 </command>
50 <inputs>
51 <conditional name="reference_source">
52 <expand macro="reference_source_selector_param" />
53 <when value="cached">
54 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
55 <validator type="unspecified_build" />
56 <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
57 </param>
58 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
59 <options from_data_table="gatk_picard_indexes">
60 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
61 </options>
62 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
63 </param>
64 </when>
65 <when value="history">
66 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
67 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
68 <options>
69 <filter type="data_meta" key="dbkey" ref="input_bam" />
70 </options>
71 </param>
72 </when>
73 </conditional>
74
75 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-known,--known &amp;lt;known&amp;gt;">
76 <conditional name="rod_bind_type">
77 <param name="rod_bind_type_selector" type="select" label="Binding Type">
78 <option value="dbsnp" selected="True">dbSNP</option>
79 <option value="snps">SNPs</option>
80 <option value="indels">INDELs</option>
81 <option value="custom">Custom</option>
82 </param>
83 <when value="dbsnp">
84 <param name="input_rod" type="data" format="vcf" label="ROD file" />
85 </when>
86 <when value="snps">
87 <param name="input_rod" type="data" format="vcf" label="ROD file" />
88 </when>
89 <when value="indels">
90 <param name="input_rod" type="data" format="vcf" label="ROD file" />
91 </when>
92 <when value="custom">
93 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
94 <param name="input_rod" type="data" format="vcf" label="ROD file" />
95 </when>
96 </conditional>
97 </repeat>
98
99 <expand macro="gatk_param_type_conditional" />
100
101 <expand macro="analysis_type_conditional">
102 <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize &amp;lt;windowSize&amp;gt;" />
103 <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to &lt;= 0 or &gt; 1 (-mismatch,--mismatchFraction &amp;lt;mismatchFraction&amp;gt;)"/>
104 <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
105 <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
106 </expand>
107 </inputs>
108 <outputs>
109 <data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" />
110 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
111 </outputs>
112 <tests>
113 <test>
114 <param name="reference_source_selector" value="history" />
115 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
116 <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" />
117 <param name="rod_bind_type_selector" value="dbsnp" />
118 <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
119 <param name="gatk_param_type_selector" value="basic" />
120 <param name="analysis_param_type_selector" value="advanced" />
121 <param name="windowSize" value="10" />
122 <param name="mismatchFraction" value="0.15" />
123 <param name="minReadsAtLocus" value="4" />
124 <param name="maxIntervalSize" value="500" />
125 <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" />
126 <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/>
127 </test>
128 </tests>
129 <help>
130 **What it does**
131
132 Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string.
133
134 For more information on local realignment around indels using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels&gt;`_.
135
136 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.
137
138 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
139
140 ------
141
142 **Inputs**
143
144 GenomeAnalysisTK: RealignerTargetCreator accepts an aligned BAM input file.
145
146
147 **Outputs**
148
149 The output is in GATK Interval format.
150
151
152 Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
153
154 -------
155
156 **Settings**::
157
158 windowSize window size for calculating entropy or SNP clusters
159 mismatchFraction fraction of base qualities needing to mismatch for a position to have high entropy; to disable set to &lt;= 0 or &gt; 1
160 minReadsAtLocus minimum reads at a locus to enable using the entropy calculation
161 maxIntervalSize maximum interval size
162
163 @CITATION_SECTION@
164 </help>
165 </tool>