Mercurial > repos > jjohnson > bcftools_stats

annotate bcftools_stats.xml @ 1:d541f5c15870 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:44:28 -0400
parents b2f7a15398b4
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b2f7a15398b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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1 <?xml version='1.0' encoding='utf-8'?>
b2f7a15398b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
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3 <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">stats</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 @PREPARE_ENV@
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12 @PREPARE_INPUT_FILES@
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13 #set $section = $sec_restrict
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14 @PREPARE_TARGETS_FILE@
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15 ## Stats section
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16 #set $section = $sec_default
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17 @PREPARE_FASTA_REF@
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18 @PREPARE_EXONS_FILE@
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19
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20 bcftools @EXECUTABLE@
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21
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22 ## Stats section
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23 #set $section = $sec_default
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24 @FASTA_REF@
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25 @EXONS_FILE@
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26 ${section.first_allele_only}
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27 #if $section.depth.set_depth == 'yes':
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28 --depth "${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size}"
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29 #end if
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30 #if $section.user_tstv:
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31 --user-tstv "${section.user_tstv}"
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32 #end if
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33 #if len($input_vcfs) == 1:
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34 ${section.split_by_ID}
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35 #end if
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36 ${section.verbose}
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37
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38 ## Stats section
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39 #set $section = $sec_restrict
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40 @APPLY_FILTERS@
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41 @COLLAPSE@
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42 @REGIONS@
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43 @SAMPLES@
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44 @TARGETS@
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45 @INCLUDE@
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46 @EXCLUDE@
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47
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48 ## Primary Input/Outputs
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49 @INPUT_FILES@
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50 > $output_file
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51 ## requires: matplotlib and pdflatex
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52 #if $plot_title:
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53 && plot-vcfstats -p 'plot_tmp/' -T $plot_title -s $output_file
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54 #end if
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55 ]]>
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56 </command>
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57 <inputs>
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58 <expand macro="macro_inputs" />
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59 <section name="sec_restrict" expanded="false" title="Restrict to">
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60 <expand macro="macro_samples" />
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61 <expand macro="macro_apply_filters" />
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62 <expand macro="macro_collapse" />
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63 <expand macro="macro_regions" />
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64 <expand macro="macro_targets" />
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65 <expand macro="macro_include" />
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66 <expand macro="macro_exclude" />
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67 </section>
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68 <section name="sec_default" expanded="true" title="Stats Options">
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69 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="1St Allele Only"
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70 help="Include only 1st allele at multiallelic sites" />
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71 <conditional name="depth">
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72 <param name="set_depth" type="select" label="depth distribution: min,max,bin_size [0,500,1]">
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73 <option value="no">use depth defaults</option>
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74 <option value="yes">set depth</option>
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75 </param>
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76 <when value="no"/>
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77 <when value="yes">
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78 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/>
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79 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />
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80 <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
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81 </when>
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82 </conditional>
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83 <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="Reference sequence" />
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84 <expand macro="macro_exons_file" />
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85 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)"
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86 help="Collect stats for sites with ID separately (known vs novel)" />
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87 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv"
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88 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >
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89 <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator>
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90
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91 </param>
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92 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose"
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93 help="Produce verbose per-site and per-sample output" />
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94 </section>
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95 <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title">
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96 <validator type="regex" message="">^\w.*\w$</validator>
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97 </param>
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98 </inputs>
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99 <outputs>
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100 <data name="output_file" format="txt"/>
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101 <data name="output_pdf" format="pdf">
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102 <filter>plot_title</filter>
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103 </data>
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104 </outputs>
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105 <tests>
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106 <test>
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107 <param name="input_files" ftype="vcf" value="stats.b.vcf,stats.a.vcf" />
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108 <output name="output_file">
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109 <assert_contents>
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110 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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111 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
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112 </assert_contents>
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113 </output>
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114 </test>
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115 <test>
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116 <param name="input_files" ftype="vcf" value="mpileup.vcf" />
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117 <output name="output_file">
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118 <assert_contents>
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119 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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120 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
1
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121 <has_text_matching expression="ST\t0\tA>C\t16"/>
0
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122 </assert_contents>
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123 </output>
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124 </test>
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125 </tests>
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126 <help><![CDATA[
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127 =====================================
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128 bcftools @EXECUTABLE@
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129 =====================================
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130
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131 Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats.
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132
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133 When two files are given, the program generates separate stats for intersection and the complements.
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134 By default only sites are compared, -s/-S must given to include also sample columns.
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135
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136 @COLLAPSE_HELP@
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137 @REGIONS_HELP@
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138 @TARGETS_HELP@
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139 @EXPRESSIONS_HELP@
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140
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141 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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142
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143 @BCFTOOLS_WIKI@
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144 ]]>
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145 </help>
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146 <expand macro="citations" />
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147 </tool>