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comparison indel_realigner.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_indel_realigner" name="Indel Realigner" version="@VERSION@.0"> 1 <tool id="gatk2_indel_realigner" name="Indel Realigner" version="@VERSION@.1">
2 <description>- perform local realignment</description> 2 <description>- perform 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( $reference_source.input_bam.metadata.bam_index ) != "None":
25 -R "${reference_source.ref_file.fields.path}" 26 -R "${reference_source.ref_file.fields.path}"
26 #end if 27 #end if
27 -LOD "${lod_threshold}" 28 -LOD "${lod_threshold}"
28 ${knowns_only} 29 ${knowns_only}
29 ' 30 '
30 31
31 #set $rod_binding_names = dict() 32 #set $rod_binding_names = dict()
32 #for $rod_binding in $rod_bind: 33 #for $rod_binding in $rod_bind:
33 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': 34 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
34 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name 35 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
35 #else 36 #else
36 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector 37 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
37 #end if 38 #end if
38 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 39 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
39 -d "-known:${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[$rod_bind_name]}" 40 -d "-known:${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]}"
40 #end for 41 #end for
41 42
43 $allow_n_cigar_reads
42 #include source=$standard_gatk_options# 44 #include source=$standard_gatk_options#
43 ##start analysis specific options 45 ##start analysis specific options
44 -d "-targetIntervals" "${target_intervals}" "${target_intervals.ext}" "gatk_target_intervals" 46 -d "-targetIntervals" "${target_intervals}" "${target_intervals.ext}" "gatk_target_intervals"
45 -p ' 47 -p '
46 --disable_bam_indexing 48 --disable_bam_indexing
58 ${analysis_param_type.no_original_alignment_tags} 60 ${analysis_param_type.no_original_alignment_tags}
59 ' 61 '
60 #end if 62 #end if
61 </command> 63 </command>
62 <inputs> 64 <inputs>
63 65
64 <conditional name="reference_source"> 66 <conditional name="reference_source">
65 <expand macro="reference_source_selector_param" /> 67 <expand macro="reference_source_selector_param" />
66 <when value="cached"> 68 <when value="cached">
67 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;"> 69 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
68 <validator type="unspecified_build" /> 70 <validator type="unspecified_build" />
108 </when> 110 </when>
109 </conditional> 111 </conditional>
110 </repeat> 112 </repeat>
111 <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" help="-LOD,--LODThresholdForCleaning &amp;lt;LODThresholdForCleaning&amp;gt;" /> 113 <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" help="-LOD,--LODThresholdForCleaning &amp;lt;LODThresholdForCleaning&amp;gt;" />
112 <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs" help="-knownsOnly"/> 114 <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs" help="-knownsOnly"/>
113 115
116 <expand macro="allow_n_cigar_reads" />
114 <expand macro="gatk_param_type_conditional" /> 117 <expand macro="gatk_param_type_conditional" />
115 118
116 <expand macro="analysis_type_conditional"> 119 <expand macro="analysis_type_conditional">
117 120
118 <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" help="-entropy,--entropyThreshold &amp;lt;entropyThreshold&amp;gt;" /> 121 <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" help="-entropy,--entropyThreshold &amp;lt;entropyThreshold&amp;gt;" />
119 <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/> 122 <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
120 <param name="consensus_determination_model" type="select" label="Consensus Determination Model" help="-model,--consensusDeterminationModel &amp;lt;consensusDeterminationModel&amp;gt;"> 123 <param name="consensus_determination_model" type="select" label="Consensus Determination Model" help="-model,--consensusDeterminationModel &amp;lt;consensusDeterminationModel&amp;gt;">
121 <option value="KNOWNS_ONLY">KNOWNS_ONLY</option> 124 <option value="KNOWNS_ONLY">KNOWNS_ONLY</option>
122 <option value="USE_READS" selected="True">USE_READS</option> 125 <option value="USE_READS" selected="True">USE_READS</option>
125 <param name="max_insert_size_for_movement" type="integer" value="3000" label="Maximum insert size of read pairs that we attempt to realign" help="-maxIsize,--maxIsizeForMovement &amp;lt;maxIsizeForMovement&amp;gt;" /> 128 <param name="max_insert_size_for_movement" type="integer" value="3000" label="Maximum insert size of read pairs that we attempt to realign" help="-maxIsize,--maxIsizeForMovement &amp;lt;maxIsizeForMovement&amp;gt;" />
126 <param name="max_positional_move_allowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,--maxPositionalMoveAllowed &amp;lt;maxPositionalMoveAllowed&amp;gt;" /> 129 <param name="max_positional_move_allowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,--maxPositionalMoveAllowed &amp;lt;maxPositionalMoveAllowed&amp;gt;" />
127 <param name="max_consensuses" type="integer" value="30" label="Max alternate consensuses to try" help="-maxConsensuses,--maxConsensuses &amp;lt;maxConsensuses&amp;gt;" /> 130 <param name="max_consensuses" type="integer" value="30" label="Max alternate consensuses to try" help="-maxConsensuses,--maxConsensuses &amp;lt;maxConsensuses&amp;gt;" />
128 <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" help="-greedy,--maxReadsForConsensuses &amp;lt;maxReadsForConsensuses&amp;gt;" /> 131 <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" help="-greedy,--maxReadsForConsensuses &amp;lt;maxReadsForConsensuses&amp;gt;" />
129 <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,--maxReadsForRealignment &amp;lt;maxReadsForRealignment&amp;gt;" /> 132 <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,--maxReadsForRealignment &amp;lt;maxReadsForRealignment&amp;gt;" />
130 <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,--noOriginalAlignmentTags"/> 133 <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,--noOriginalAlignmentTags"/>
131 </expand> 134 </expand>
132 </inputs> 135 </inputs>
133 <outputs> 136 <outputs>
134 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" /> 137 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
135 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 138 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
153 <param name="max_positional_move_allowed" value="200" /> 156 <param name="max_positional_move_allowed" value="200" />
154 <param name="max_consensuses" value="30" /> 157 <param name="max_consensuses" value="30" />
155 <param name="max_reads_for_consensuses" value="120" /> 158 <param name="max_reads_for_consensuses" value="120" />
156 <param name="max_reads_for_realignment" value="20000" /> 159 <param name="max_reads_for_realignment" value="20000" />
157 <param name="no_original_alignment_tags" /> 160 <param name="no_original_alignment_tags" />
158 <output name="output_bam" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" lines_diff="2" /> 161 <output name="output_bam" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" lines_diff="2" />
159 <output name="output_log" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains" compare="contains" /> 162 <output name="output_log" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains" compare="contains" />
160 </test> 163 </test>
161 </tests> 164 </tests>
162 <help> 165 <help>
163 **What it does** 166 **What it does**