Mercurial > repos > jjohnson > bcftools_filter

annotate bcftools_filter.xml @ 0:442f9d982db3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:47:47 -0400
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children 201536a80600
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442f9d982db3 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'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
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3 <description>Apply fixed-threshold filters</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">filter</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_FILE@
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13 #set $section = $sec_restrict
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14 @PREPARE_TARGETS_FILE@
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15
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16 bcftools @EXECUTABLE@
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17
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18 ## Filter section
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19 #set $section = $sec_filter
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20 #if $section.SnpGap:
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21 --SnpGap "${section.SnpGap}"
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22 #end if
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23 #if $section.IndelGap:
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24 --IndelGap "${section.IndelGap}"
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25 #end if
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26 #if $section.mode:
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27 #set $mode = str($section.mode).replace(',','')
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28 --mode '$mode'
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29 #end if
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30 #if $section.soft_filter:
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31 --soft-filter "${section.soft_filter}"
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32 #end if
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33 #if $section.select_set_GTs:
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34 --set-GTs "${section.select_set_GTs}"
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35 #end if
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36
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37 #set $section = $sec_restrict
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38 @REGIONS@
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39 @TARGETS@
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40 @INCLUDE@
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41 @EXCLUDE@
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42
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43 @OUTPUT_TYPE@
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44 @THREADS@
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45
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46 ## Primary Input/Outputs
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47 @INPUT_FILE@
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48 > "$output_file"
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49 ]]>
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50 </command>
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51 <inputs>
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52 <expand macro="macro_input" />
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53 <section name="sec_restrict" expanded="false" title="Restrict to">
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54 <expand macro="macro_regions" />
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55 <expand macro="macro_targets" />
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56 <expand macro="macro_include" />
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57 <expand macro="macro_exclude" />
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58 </section>
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59 <section name="sec_filter" expanded="false" title="Filter Options">
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60 <param name="SnpGap" type="integer" label="Snpgap" optional="True" help="(-g) Filter SNPs within &lt;int&gt; base pairs of an indel" />
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61 <param name="IndelGap" type="integer" label="Indelgap" optional="True" help="(-G) Filter clusters of indels separated by &lt;int&gt; or fewer base pairs allowing only one to pass" />
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62 <param name="mode" type="select" label="Mode FILTER annotation" optional="true" multiple="true" display="checkboxes">
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63 <help>(-m)
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64 The default mode replaces existing filters of failed sites with a new FILTER string
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65 while leaving sites which pass untouched when non-empty
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66 and setting to "PASS" when the FILTER string is absent.
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67 </help>
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68 <option value="+">(+) append new FILTER strings of failed sites instead of replacing them</option>
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69 <option value="x">(x) resets filters of sites which pass to "PASS"</option>
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70 </param>
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71 <param name="soft_filter" type="text" value="" label="Soft Filter" optional="true">
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72 <help><![CDATA[ (-s)
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73 Annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d").
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74 ]]></help>
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75 </param>
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76 <param name="select_set_GTs" type="select" ladel="Set genotypes of failed samples" optional="true" help="(-S)">
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77 <option value=".">to missing (.)</option>
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78 <option value="0">to REF (0)</option>
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79 </param>
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80 </section>
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81 <expand macro="macro_select_output_type" />
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82 </inputs>
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83 <outputs>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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diff changeset
84 <expand macro="macro_vcf_output"/>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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85 </outputs>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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86 <tests>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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87 <test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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88 <param name="input_file" ftype="vcf" value="filter.1.vcf" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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89 <param name="mode" value="x" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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90 <param name="SnpGap" value="2" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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91 <param name="IndelGap" value="2" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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92 <param name="output_type" value="v" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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93 <output name="output_file">
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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94 <assert_contents>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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95 <has_text text="PASS" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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96 <not_has_text text="1006" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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97 </assert_contents>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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98 </output>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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99 </test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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100 <test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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101 <param name="input_file" ftype="vcf" value="filter.2.vcf" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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102 <param name="exclude" value="QUAL==59.2 || (INDEL=0 &amp; (FMT/GQ=25 | FMT/DP=10))" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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103 <param name="soft_filter" value="Modified" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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104 <param name="select_set_GTs" value="." />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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105 <param name="output_type" value="v" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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106 <output name="output_file">
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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107 <assert_contents>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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108 <has_text text="Modified" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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109 <has_text text="AN=2;AC=1" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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110 <has_text_matching expression="TAAAA\tTA,T\t61.5\tModified" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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111 </assert_contents>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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112 </output>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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113 </test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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114 <test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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115 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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116 <param name="exclude" value="DP=19" />
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117 <param name="output_type" value="v" />
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118 <output name="output_file">
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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119 <assert_contents>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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120 <not_has_text text="3162006" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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121 <has_text text="3162007" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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122 </assert_contents>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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123 </output>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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124 </test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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125
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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126 <test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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127 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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128 <param name="exclude" value="DP=19" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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129 <param name="soft_filter" value="XX" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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130 <param name="output_type" value="v" />
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131 <output name="output_file">
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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132 <assert_contents>
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133 <has_text_matching expression="\tXX\tDP=19" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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134 <has_text_matching expression="\tq20\tAO" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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135 </assert_contents>
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136 </output>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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137 </test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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138 <test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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139 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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140 <param name="exclude" value="DP=19" />
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141 <param name="soft_filter" value="XX" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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142 <param name="mode" value="+" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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143 <param name="output_type" value="v" />
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144 <output name="output_file">
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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145 <assert_contents>
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146 <has_text_matching expression="\tq20;XX\tDP=19" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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147 <has_text_matching expression="\tq20\tAO" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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148 </assert_contents>
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149 </output>
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150 </test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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151 <test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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152 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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153 <param name="exclude" value="DP=19" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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154 <param name="soft_filter" value="XX" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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155 <param name="mode" value="x" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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156 <param name="output_type" value="v" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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157 <output name="output_file">
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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158 <assert_contents>
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159 <has_text_matching expression="\tXX\tDP=19" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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160 <has_text_matching expression="\tPASS\tAO" />
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161 </assert_contents>
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162 </output>
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163 </test>
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164 <test>
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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165 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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166 <param name="exclude" value="DP=19" />
442f9d982db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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167 <param name="soft_filter" value="XX" />
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168 <param name="mode" value="\+x" />
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169 <param name="output_type" value="v" />
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170 <output name="output_file">
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171 <assert_contents>
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172 <has_text_matching expression="\tq20;XX\tDP=19" />
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173 <has_text_matching expression="\tPASS\tAO" />
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174 </assert_contents>
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175 </output>
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176 </test>
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177 <test>
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178 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
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179 <param name="exclude" value="FMT/GT=&quot;0/2&quot;" />
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180 <param name="output_type" value="v" />
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181 <output name="output_file">
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182 <assert_contents>
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183 <not_has_text text="3162006" />
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184 <has_text text="3162007" />
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185 </assert_contents>
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186 </output>
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187 </test>
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188 <test>
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189 <param name="input_file" ftype="vcf" value="filter.2.vcf" />
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190 <param name="include" value="FMT/GT=&quot;0/0&quot; &amp;&amp; AC[*]=2" />
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191 <param name="output_type" value="v" />
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192 <output name="output_file">
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193 <assert_contents>
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194 <has_text text="AN=4;AC=2" />
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195 <not_has_text text="AN=4;AC=0" />
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196 </assert_contents>
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197 </output>
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198 </test>
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199 </tests>
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200 <help><![CDATA[
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201 =====================================
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202 bcftools @EXECUTABLE@
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203 =====================================
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204
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205 Apply fixed-threshold filters.
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206
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207 @REGIONS_HELP@
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208 @TARGETS_HELP@
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209 @EXPRESSIONS_HELP@
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210
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211
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212 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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213
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214 @BCFTOOLS_WIKI@
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215 ]]>
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216 </help>
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217 <expand macro="citations" />
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218 </tool>