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annotate tools/naive_variant_detector.xml @ 3:b59e4da0cb70

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Update pyBam* dependencies revisions.
author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 14 May 2013 12:53:54 -0400
parents 55b4460cd0ce
children 1c23da12b768
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1 <tool id="naive_variant_detector" name="Naive Variant Detector" version="0.0.1">
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2 <description>on BAM files</description>
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3 <requirements>
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4 <requirement type="package" version="1.7.1">numpy</requirement>
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5 <requirement type="package" version="0.0.1">pyBamParser</requirement>
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6 <requirement type="package" version="0.0.1">pyBamTools</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" err_level="fatal" />
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10 <exit_code range=":-1" err_level="fatal" />
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11 </stdio>
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12 <command interpreter="python">naive_variant_detector.py
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13 -o "${output_vcf}"
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14
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15 #for $input_bam in $reference_source.input_bams:
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16 -b "${input_bam.input_bam}"
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17 -i "${input_bam.input_bam.metadata.bam_index}"
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18 #end for
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19
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20 #if $reference_source.reference_source_selector != "history":
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21 -r "${reference_source.ref_file.fields.path}"
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22 #elif $reference_source.ref_file:
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23 -r "${reference_source.ref_file}"
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24 #end if
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25
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26 #for $region in $regions:
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27 --region "${region.chromosome}:${region.start}-${region.end}"
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28 #end for
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29
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30 ${variants_only}
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31
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32 ${use_strand}
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33
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34 --ploidy "${$ploidy}"
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35
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36 --min_support_depth "${min_support_depth}"
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37
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38 #if str($min_base_quality):
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39 --min_base_quality "${min_base_quality}"
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40 #end if
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41
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42 #if str($min_mapping_quality):
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43 --min_mapping_quality "${min_mapping_quality}"
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44 #end if
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45
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46 --coverage_dtype "${coverage_dtype}"
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47
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48 </command>
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49 <inputs>
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50 <conditional name="reference_source">
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51 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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52 <option value="cached">Locally cached</option>
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53 <option value="history">History</option>
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54 </param>
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55 <when value="cached">
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56 <repeat name="input_bams" title="BAM file" min="1" >
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57 <param name="input_bam" type="data" format="bam" label="BAM file">
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58 <validator type="unspecified_build" />
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59 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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60 </param>
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61 </repeat>
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62 <param name="ref_file" type="select" label="Using reference genome" >
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63 <options from_data_table="sam_fa_indexes">
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64 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
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65 </options>
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66 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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67 </param>
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68 </when>
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69 <when value="history"> <!-- FIX ME!!!! -->
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70 <repeat name="input_bams" title="BAM file" min="1" >
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71 <param name="input_bam" type="data" format="bam" label="BAM file" >
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72 </param>
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73 </repeat>
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74 <param name="ref_file" type="data" format="fasta" label="Using reference file" optional="True" />
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75 </when>
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76 </conditional>
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77
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78 <repeat name="regions" title="Restrict to regions" min="0" >
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79 <param name="chromosome" type="text" value="" optional="False" label="Chromosome" />
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80 <param name="start" type="integer" value="" optional="True" label="Start" />
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81 <param name="end" type="integer" value="" optional="True" label="End" />
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82 </repeat>
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83
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84 <!-- TODO: enhance filtering -->
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85 <param name="min_support_depth" type="integer" value="0" min="0" label="Minimum number of reads needed to consider a REF/ALT" />
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86 <param name="min_base_quality" type="integer" value="" label="Minimum base quality" optional="True" />
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87 <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" />
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88
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89
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90 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
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91 <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with with possible alternate alleles"/>
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92
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93 <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
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94
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95 <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM">
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96 <option value="uint8" selected="True">uint8</option>
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97 <option value="uint16">uint16</option>
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98 <option value="uint32">uint32</option>
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99 <option value="uint64">uint64</option>
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100 </param>
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101
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102 </inputs>
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103 <outputs>
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104 <data format="vcf" name="output_vcf" />
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105 </outputs>
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106 <help>
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107 **What it does**
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108
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109 This tool is a naive variant detector.
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110
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111 ------
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112
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113 **Inputs**
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114
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115 Accepts one or more BAM input files.
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116
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117
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118 **Outputs**
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119
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120 The output is in VCF format.
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121
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122 ------
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123
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124 **Citation**
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125
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126 If you use this tool, please cite Blankenberg D, et al. *In preparation.*
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127
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128 </help>
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129 <tests>
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130 <test>
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131 <param name="reference_source_selector" value="history" />
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132 <param name="input_bam" value="test-data/fake_phiX174_reads_1.bam" ftype="bam" />
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133 <param name="ref_file" value="test-data/phiX174.fasta" ftype="fasta" />
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134 <param name="min_support_depth" value="0" />
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135 <param name="min_base_quality" value="" />
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136 <param name="min_mapping_quality" value="" />
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137 <param name="ploidy" value="2" />
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138 <param name="variants_only" value="False" />
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139 <param name="use_strand" value="False" />
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140 <param name="coverage_dtype" value="uint8" />
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141 <output name="output_vcf" file="test-data/fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
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142 </test>
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143 </tests>
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144
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145 </tool>