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comparison samtools_mpileup.xml @ 4:5872c9894a37 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_mpileup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:24:45 -0500
parents da0203c3461a
children 483949f5c3b0
comparison
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3:da0203c3461a 4:5872c9894a37
1 <tool id="samtools_mpileup" name="MPileup" version="2.1"> 1 <tool id="samtools_mpileup" name="MPileup" version="2.1.1">
2 <description>call variants</description> 2 <description>call variants</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
16 #if $reference_source.reference_source_selector != "history": 16 #if $reference_source.reference_source_selector != "history":
17 -f "${reference_source.ref_file.fields.path}" 17 -f "${reference_source.ref_file.fields.path}"
18 #else: 18 #else:
19 -f "${reference_source.ref_file}" 19 -f "${reference_source.ref_file}"
20 #end if 20 #end if
21 #for $i, $input_bam in enumerate( $reference_source.input_bams ): 21 #for $bam in $reference_source.input_bam:
22 "${input_bam.input_bam}" 22 "${bam}"
23 #end for 23 #end for
24 #if str( $advanced_options.advanced_options_selector ) == "advanced": 24 #if str( $advanced_options.advanced_options_selector ) == "advanced":
25 #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter": 25 #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":
26 #if $advanced_options.filter_by_flags.require_flags: 26 #if $advanced_options.filter_by_flags.require_flags:
27 --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])} 27 --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])}
48 -q "${advanced_options.minimum_mapping_quality}" 48 -q "${advanced_options.minimum_mapping_quality}"
49 -Q "${advanced_options.minimum_base_quality}" 49 -Q "${advanced_options.minimum_base_quality}"
50 #if str( $advanced_options.region_string ): 50 #if str( $advanced_options.region_string ):
51 -r "${advanced_options.region_string}" 51 -r "${advanced_options.region_string}"
52 #end if 52 #end if
53 53
54 #end if 54 #end if
55 #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation': 55 #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation':
56 ## 56 ##
57 57
58 ${genotype_likelihood_computation_type.output_format} 58 ${genotype_likelihood_computation_type.output_format}
59 ${genotype_likelihood_computation_type.compressed} 59 ${genotype_likelihood_computation_type.compressed}
60 60
61 #if str( $genotype_likelihood_computation_type.output_tags ) != "None": 61 #if str( $genotype_likelihood_computation_type.output_tags ) != "None":
62 --output-tags "${genotype_likelihood_computation_type.output_tags}" 62 --output-tags "${genotype_likelihood_computation_type.output_tags}"
63 #end if 63 #end if
64 64
65 #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling': 65 #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling':
75 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ] ) }" 75 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ] ) }"
76 #end if 76 #end if
77 #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling': 77 #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling':
78 -I 78 -I
79 #end if 79 #end if
80 80
81 81
82 #else: 82 #else:
83 ${genotype_likelihood_computation_type.base_position_on_reads} 83 ${genotype_likelihood_computation_type.base_position_on_reads}
84 ${genotype_likelihood_computation_type.output_mapping_quality} 84 ${genotype_likelihood_computation_type.output_mapping_quality}
85 #end if 85 #end if
86 --output "$output_mpileup" 2> "$output_log" 86 --output "$output_mpileup" 2> "$output_log"
91 <param label="Choose the source for the reference genome" name="reference_source_selector" type="select"> 91 <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
92 <option value="cached">Use a built-in genome</option> 92 <option value="cached">Use a built-in genome</option>
93 <option value="history">Use a genome from the history</option> 93 <option value="history">Use a genome from the history</option>
94 </param> 94 </param>
95 <when value="cached"> 95 <when value="cached">
96 <repeat min="1" name="input_bams" title="BAM file"> 96 <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True">
97 <param format="bam" label="BAM file" name="input_bam" type="data"> 97 <validator type="unspecified_build" />
98 <validator type="unspecified_build" /> 98 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
99 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" /> 99 </param>
100 </param>
101 </repeat>
102 <param label="Using reference genome" name="ref_file" type="select"> 100 <param label="Using reference genome" name="ref_file" type="select">
103 <options from_data_table="fasta_indexes" /> 101 <options from_data_table="fasta_indexes" />
104 </param> 102 </param>
105 </when> 103 </when>
106 <when value="history"> 104 <when value="history">
107 <repeat min="1" name="input_bams" title="BAM file"> 105 <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True">
108 <param format="bam" label="BAM file" name="input_bam" type="data"> 106 <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
109 <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> 107 </param>
110 </param>
111 </repeat>
112 <param format="fasta" label="Using reference genome" name="ref_file" type="data" /> 108 <param format="fasta" label="Using reference genome" name="ref_file" type="data" />
113 </when> 109 </when>
114 </conditional> 110 </conditional>
115 <conditional name="genotype_likelihood_computation_type"> 111 <conditional name="genotype_likelihood_computation_type">
116 <param label="Genotype Likelihood Computation" name="genotype_likelihood_computation_type_selector" type="select"> 112 <param label="Genotype Likelihood Computation" name="genotype_likelihood_computation_type_selector" type="select">
151 <param label="Platform to use for INDEL candidates" name="platform_entry" type="text" value="" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/> 147 <param label="Platform to use for INDEL candidates" name="platform_entry" type="text" value="" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
152 </repeat> 148 </repeat>
153 </when> 149 </when>
154 <when value="do_not_perform_indel_calling" /> 150 <when value="do_not_perform_indel_calling" />
155 </conditional> 151 </conditional>
156 152
157 </when> 153 </when>
158 <when value="do_not_perform_genotype_likelihood_computation"> 154 <when value="do_not_perform_genotype_likelihood_computation">
159 <param checked="False" falsevalue="" label="Output base positions on reads" name="base_position_on_reads" truevalue="-O" type="boolean" help="--output-BP"/> 155 <param checked="False" falsevalue="" label="Output base positions on reads" name="base_position_on_reads" truevalue="-O" type="boolean" help="--output-BP"/>
160 <param checked="False" falsevalue="" label="Output mapping quality" name="output_mapping_quality" truevalue="-s" type="boolean" help="--output-MQ"/> 156 <param checked="False" falsevalue="" label="Output mapping quality" name="output_mapping_quality" truevalue="-s" type="boolean" help="--output-MQ"/>
161 </when> 157 </when>
286 </tests> 282 </tests>
287 <help> 283 <help>
288 <![CDATA[ 284 <![CDATA[
289 **What it does** 285 **What it does**
290 286
291 Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. 287 Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample.
292 288
293 ------ 289 ------
294 290
295 **Input options**:: 291 **Input options**::
296 292