Mercurial > repos > iuc > ngsutils_bam_filter

annotate bam_filter.xml @ 4:aecfe10118ed draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 89a8c896bdc435acb5e5c490f4deae4a4ed9607a
author iuc
date Fri, 17 Nov 2017 05:17:42 -0500
parents 9b9ae5963d3c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9b9ae5963d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
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1 <tool id="ngsutils_bam_filter" name="BAM filter" version="@WRAPPER_VERSION@">
0
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2 <description>Removes reads from a BAM file based on criteria</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version" />
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9 <command><![CDATA[
3
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10 ## If the tool is executed with no filtering option,
9b9ae5963d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
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11 ## the default parameters simply copy over the input file
9b9ae5963d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
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12 if grep -q "\w" '${parameters}'; then
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13 python '$__tool_directory__/filter.py'
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14 '$infile'
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15 '$outfile'
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16 `cat ${parameters}`;
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17 else
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18 cp '$infile' '$outfile';
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19 fi
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20 ]]></command>
0
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21 <configfiles>
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22 <configfile name="parameters"><![CDATA[
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23 #if $minlen:
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24 -minlen $minlen
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25 #end if
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26 #if $maxlen
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27 -maxlen $maxlen
9b9ae5963d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
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28 #end if
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29 $mapped
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30 $unmapped
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31 $properpair
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32 $noproperpair
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33 #if $mask:
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34 -mask ${mask}
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35 #end if
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36 #if int($uniq) > -1:
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37 -uniq
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38 #if int($uniq) > 0:
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39 $uniq
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40 #end if
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41 #end if
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42 $uniq_start
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43 #if $mismatch:
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44 -mismatch $mismatch
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45 #end if
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46 $nosecondary
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47 $noqcfail
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48 $nopcrdup
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49 #if $excludebed:
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50 -excludebed ${excludebed} $ignore_strand
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51 #end if
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52 #if $includebed:
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53 -includebed ${includebed} $ignore_strand
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54 #end if
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55 #if $includeref:
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56 -includeref ${includeref}
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57 #end if
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58 #if $excluderef:
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59 -excluderef ${excluderef}
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60 #end if
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61 #if $maximum_mismatch_ratio
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62 -maximum_mismatch_ratio $maximum_mismatch_ratio
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63 #end if
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64 ]]></configfile>
0
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65 </configfiles>
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66 <inputs>
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67 <param name="infile" type="data" format="bam" label="Select BAM dataset" />
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68 <param argument="-minlen" type="integer" value="" optional="True" min="0"
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69 label="Remove reads that are smaller than"
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70 help="in bp"/>
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71 <param argument="-maxlen" type="integer" value="" optional="True" min="0"
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72 label="Remove reads that are larger than"
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73 help="in bp"/>
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74 <param argument="-mapped" truevalue="-mapped" type="boolean" falsevalue=""
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75 label="Keep only mapped reads"
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76 help="" />
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77 <param argument="-unmapped" truevalue="-unmapped" type="boolean" falsevalue=""
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78 label="Keep only unmapped reads"
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79 help="" />
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80 <param argument="-properpair" truevalue="-properpair" type="boolean" falsevalue=""
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81 label="Keep only properly paired reads"
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82 help="both mapped, correct orientation, flag set in BAM" />
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83 <param argument="-noproperpair" truevalue="-noproperpair" type="boolean" falsevalue=""
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84 label="Discard properly paired reads"
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85 help="" />
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86 <param argument="-mask" type="text" value="" optional="True" label="Remove reads that match the mask"
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87 help="e.g. 0x400, 0x2" />
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88
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89 <param argument="-uniq" type="integer" value="-1" optional="True" min="-1"
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90 label="Remove reads that have the same sequence"
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91 help="up to the Nth nucleotide starting from the 5prime end. -1 means do not filter, 0 means check along the entire read,
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92 10 would make filter reads that are unique over the first 10 nucleotides."/>
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93
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94 <param argument="-uniq_start" truevalue="-uniq_start" type="boolean" falsevalue=""
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95 label="Remove reads that start at the same position"
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96 help="Use only for low-coverage samples" />
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97
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98 <param argument="-mismatch" type="integer" value="" optional="True" min="0"
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99 label="Remove reads with that many mismatches"
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100 help="Indels always counts as 1 regardless of length. Requires NM tag to be set."/>
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101
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102 <param argument="-nosecondary" truevalue="-nosecondary" type="boolean" falsevalue=""
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103 label="Remove secondary alignment reads"
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104 help="Remove reads flagged with 0x100" />
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105 <param argument="-noqcfail" truevalue="-noqcfail" type="boolean" falsevalue=""
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106 label="Remove reads that do not pass the quality control"
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107 help="Remove reads flagged with 0x200" />
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108 <param argument="-nopcrdup" truevalue="-nopcrdup" type="boolean" falsevalue=""
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109 label="Remove reads that are marked as PCR dupicates "
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110 help="Remove reads flagged with 0x400" />
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111
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112 <param argument="-excludebed" type="data" optional="True" format="bed" label="Remove reads that are in any of the regions" />
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113 <param argument="-includebed" type="data" optional="True" format="bed" label="Remove reads that are NOT any of the regions" />
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114 <param name="ignore_strand" truevalue="nostrand" type="boolean" falsevalue=""
1
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115 label="Strand information from BED file is ignored"
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116 help="Affects -excludebed and -includebed." />
0
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117
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118 <param argument="-includeref" type="text" value="" optional="True" label="Exclude reads NOT mapped to a reference"
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119 help="" />
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120 <param argument="-excluderef" type="text" value="" optional="True" label="Exclude reads mapped to a particular reference"
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121 help="e.g. chrM, or _dup chromosomes" />
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122
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123 <param argument="-maximum_mismatch_ratio" type="float" value="" optional="True" min="0.0" max="1.0"
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124 label="Filter by maximum mismatch ratio"
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125 help="fraction of length"/>
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126 </inputs>
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127 <outputs>
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128 <data format="bam" name="outfile" />
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129 </outputs>
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130 <tests>
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131 <test>
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132 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
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133 <param name="minlen" value="100"/>
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134 <param name="maximum_mismatch_ratio" value="0.02"/>
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135 <output name="outfile" file="ngsutils_bam_filter_result1.bam" ftype="bam" />
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136 </test>
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137 <test>
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138 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
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139 <param name="minlen" value="250"/>
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140 <param name="properpair" value="True"/>
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141 <output name="outfile" file="ngsutils_bam_filter_result2.bam" ftype="bam" />
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142 </test>
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143 <test>
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144 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
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145 <param name="minlen" value="100"/>
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146 <param name="nosecondary" value="True"/>
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147 <param name="noqcfail" value="True"/>
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148 <param name="nopcrdup" value="True"/>
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149 <output name="outfile" file="ngsutils_bam_filter_result3.bam" ftype="bam" />
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150 </test>
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151 <test>
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152 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
1
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153 <output name="outfile" file="ngsutils_bam_filter_input4.bam" ftype="bam" />
0
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154 </test>
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155 <test>
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156 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
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157 <param name="mask" value="0x40"/>
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158 <output name="outfile" file="ngsutils_bam_filter_result5.bam" ftype="bam" />
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159 </test>
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160 <test>
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161 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
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162 <param name="excludebed" value="exclude.bed" ftype="bed"/>
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163 <param name="ignore_strand" value="True" />
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164 <output name="outfile" file="ngsutils_bam_filter_result6.bam" ftype="bam" />
0
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165 </test>
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166 </tests>
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167 <help><![CDATA[
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168 Removes reads from a BAM file based on criteria.
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169
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170 Given a BAM file, this tool will discard reads that did not meet the selected filtering criteria
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171 The output is another BAM file with the reads not matching the criteria removed.
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172
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173 Note: this does not adjust tag values reflecting any filtering. (for example:
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174 if a read mapped to two locations (IH:i:2), and one was removed by
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175 filtering, the IH:i tag would still read IH:i:2).
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176
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177 Currently, the available filters are:
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178
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179 +--------------------------------+-------------------------------------------------+
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180 | Agument | Description |
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181 +================================+=================================================+
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182 | -minlen val | Remove reads that are smaller than {val} |
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183 +--------------------------------+-------------------------------------------------+
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184 | -maxlen val | Remove reads that are larger than {val} |
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185 +--------------------------------+-------------------------------------------------+
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186 | -mapped | Keep only mapped reads |
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187 +--------------------------------+-------------------------------------------------+
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188 | -unmapped | Keep only unmapped reads |
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189 +--------------------------------+-------------------------------------------------+
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190 | -properpair | Keep only properly paired reads (both mapped, |
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191 | | correct orientation, flag set in BAM) |
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192 +--------------------------------+-------------------------------------------------+
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193 | -noproperpair | Keep only not-properly paired reads |
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194 +--------------------------------+-------------------------------------------------+
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195 | -mask bitmask | Remove reads that match the mask (e.g. 0x400) |
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196 +--------------------------------+-------------------------------------------------+
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197 | -uniq {length} | Remove reads that are have the same sequence |
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198 | | Note: BAM file should be sorted |
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199 | | (up to an optional length) |
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200 +--------------------------------+-------------------------------------------------+
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201 | -uniq_start | Remove reads that start at the same position |
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202 | | Note: BAM file should be sorted |
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203 | | (Use only for low-coverage samples) |
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204 +--------------------------------+-------------------------------------------------+
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205 |-mismatch num | Number of mismatches or indels |
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206 | | indel always counts as 1 regardless of length |
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207 | | (requires NM tag in reads) |
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208 +--------------------------------+-------------------------------------------------+
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209 |-nosecondary | Remove reads that have the 0x100 flag set |
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210 +--------------------------------+-------------------------------------------------+
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211 |-noqcfail | Remove reads that have the 0x200 flag set |
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212 +--------------------------------+-------------------------------------------------+
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213 |-nopcrdup | Remove reads that have the 0x400 flag set |
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214 +--------------------------------+-------------------------------------------------+
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215 |-excludebed file.bed {nostrand} | Remove reads that are in any of the regions |
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216 | | from the given BED file. If 'nostrand' is given,|
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217 | | strand information from the BED file is ignored.|
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218 +--------------------------------+-------------------------------------------------+
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219 |-includebed file.bed {nostrand} | Remove reads that are NOT any of the regions |
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220 | | from the given BED file. If 'nostrand' is given,|
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221 | | strand information from the BED file is ignored.|
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222 | | Note: If this is a large dataset, use |
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223 | | "bamutils extract" instead. |
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224 +--------------------------------+-------------------------------------------------+
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225 | -includeref refname | Exclude reads NOT mapped to a reference |
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226 +--------------------------------+-------------------------------------------------+
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227 | -excluderef refname | Exclude reads mapped to a particular reference |
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228 | | (e.g. chrM, or _dup chromosomes) |
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229 +--------------------------------+-------------------------------------------------+
3
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230 ]]></help>
0
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231 </tool>