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comparison realigner_target_creator.xml @ 6:35c00763cb5c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
author iuc
date Mon, 04 Jun 2018 05:38:15 -0400
parents f244b8209eb8
children
comparison
equal deleted inserted replaced
5:84584664264c 6:35c00763cb5c
1 <tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="@VERSION@.0"> 1 <tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="@VERSION@.1">
2 <description>for use in local realignment</description> 2 <description>for use in local realignment</description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>gatk2_macros.xml</import> 4 <import>gatk2_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
7 <command interpreter="python"> 8 <command interpreter="python">
8 gatk2_wrapper.py 9 gatk2_wrapper.py
9 --stdout "${output_log}" 10 --stdout "${output_log}"
10 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" 11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
11 #if str( $reference_source.input_bam.metadata.bam_index ) != "None": 12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
35 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector 36 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
36 #end if 37 #end if
37 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 38 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
38 -d "-known:${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[$rod_bind_name]}" 39 -d "-known:${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]}"
39 #end for 40 #end for
40 41
42 $allow_n_cigar_reads
41 #include source=$standard_gatk_options# 43 #include source=$standard_gatk_options#
42 ##start analysis specific options 44 ##start analysis specific options
43 #if $analysis_param_type.analysis_param_type_selector == "advanced": 45 #if $analysis_param_type.analysis_param_type_selector == "advanced":
44 -p ' 46 -p '
45 --minReadsAtLocus "${analysis_param_type.minReadsAtLocus}" 47 --minReadsAtLocus "${analysis_param_type.minReadsAtLocus}"
71 <filter type="data_meta" key="dbkey" ref="input_bam" /> 73 <filter type="data_meta" key="dbkey" ref="input_bam" />
72 </options> 74 </options>
73 </param> 75 </param>
74 </when> 76 </when>
75 </conditional> 77 </conditional>
76 78
77 <repeat name="rod_bind" title="Known Variants" help="Using data sets of known variants (-known,--known &amp;lt;known&amp;gt;)"> 79 <repeat name="rod_bind" title="Known Variants" help="Using data sets of known variants (-known,--known &amp;lt;known&amp;gt;)">
78 <conditional name="rod_bind_type"> 80 <conditional name="rod_bind_type">
79 <param name="rod_bind_type_selector" type="select" label="Variant Type"> 81 <param name="rod_bind_type_selector" type="select" label="Variant Type">
80 <option value="dbsnp" selected="True">dbSNP</option> 82 <option value="dbsnp" selected="True">dbSNP</option>
81 <option value="snps">SNPs</option> 83 <option value="snps">SNPs</option>
82 <option value="indels">INDELs</option> 84 <option value="indels">INDELs</option>
83 <option value="custom">Custom</option> 85 <option value="custom">Custom</option>
84 </param> 86 </param>
85 <when value="dbsnp"> 87 <when value="dbsnp">
86 <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" /> 88 <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" />
95 <param name="custom_rod_name" type="text" value="Unknown" label="Customer's variant file" /> 97 <param name="custom_rod_name" type="text" value="Unknown" label="Customer's variant file" />
96 <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" /> 98 <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" />
97 </when> 99 </when>
98 </conditional> 100 </conditional>
99 </repeat> 101 </repeat>
100 102
103 <expand macro="allow_n_cigar_reads" />
101 <expand macro="gatk_param_type_conditional" /> 104 <expand macro="gatk_param_type_conditional" />
102 105
103 <expand macro="analysis_type_conditional"> 106 <expand macro="analysis_type_conditional">
104 <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;" /> 107 <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)"
105 <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;)"/> 108 help="-window,--windowSize &amp;lt;windowSize&amp;gt;" />
106 <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;" /> 109 <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)"
110 help="to disable set to &lt;= 0 or &gt; 1 (-mismatch,--mismatchFraction &amp;lt;mismatchFraction&amp;gt;)"/>
111 <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)"
112 help="-minReads,--minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
107 <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" /> 113 <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
108 </expand> 114 </expand>
109 </inputs> 115 </inputs>
110 <outputs> 116 <outputs>
111 <data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" /> 117 <data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" />
122 <param name="analysis_param_type_selector" value="advanced" /> 128 <param name="analysis_param_type_selector" value="advanced" />
123 <param name="windowSize" value="10" /> 129 <param name="windowSize" value="10" />
124 <param name="mismatchFraction" value="0.15" /> 130 <param name="mismatchFraction" value="0.15" />
125 <param name="minReadsAtLocus" value="4" /> 131 <param name="minReadsAtLocus" value="4" />
126 <param name="maxIntervalSize" value="500" /> 132 <param name="maxIntervalSize" value="500" />
127 <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" /> 133 <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" />
128 <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/> 134 <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/>
129 </test> 135 </test>
130 </tests> 136 </tests>
131 <help> 137 <help>
132 **What it does** 138 **What it does**