Mercurial > repos > devteam > samtool_filter2

annotate samtool_filter2.xml @ 15:1ea3b8a4c2fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
author devteam
date Fri, 20 Jan 2017 04:51:24 -0500
parents cc2b231ab5e1
children 160964255888
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1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.2">
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2 <description>files on FLAG MAPQ RG LN or by region</description>
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3 <requirements>
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4 <requirement type="package" version="1.2">samtools</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command>
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10 <![CDATA[
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11 ##set up input files, regions requires input.bam and input.bai
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12 #if $input1.is_of_type('bam')
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13 #set $input = 'input.bam'
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14 ln -s '$input1' $input &&
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15 ln -s '$input1.metadata.bam_index' input.bai &&
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16 #elif $input1.is_of_type('sam')
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17 #set $input = 'input.sam'
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18 ln -s '$input1' $input &&
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19 #end if
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20 samtools view $possibly_select_inverse '$output1' $header
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21
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22 #if $input1.is_of_type('sam')
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23 -S
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24 #end if
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25
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26 #if str($outputtype) == 'bam'
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27 -b
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28 #end if
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29
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30 #if str($mapq)
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31 -q $mapq
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32 #end if
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33 #if $flag.filter == 'yes'
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34 #if str($flag.reqBits) != 'None'
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35 #set $reqs = str($flag.reqBits).split(',')
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36 #set $reqFlag = 0
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37 #for $xn in $reqs:
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38 #set $reqFlag += int($xn, 16)
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39 #end for
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40 -f $hex($reqFlag)
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41 #end if
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42 #if str($flag.skipBits) != 'None'
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43 #set $skips = str($flag.skipBits).split(',')
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44 #set $skipFlag = 0
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45 #for $xn in $skips:
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46 #set $skipFlag += int(xn,16)
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47 #end for
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48 -F $hex($skipFlag)
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49 #end if
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50 #end if
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51 #if str($read_group).strip()
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52 -r '$read_group'
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53 #end if
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54 #if str($library).strip()
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55 -l '$library'
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56 #end if
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57 #if $bed_file
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58 -L '$bed_file'
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59 #end if
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60 $input
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61 #if str($regions).strip() and $input1.is_of_type('bam')
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62 '$regions'
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63 #end if
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64 ## need to redirect stderr message so galaxy does not think this failed
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65 2>&1
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66 ]]>
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67 </command>
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68 <inputs>
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69 <param name="input1" type="data" format="sam,bam" label="SAM or BAM file to filter" />
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70 <param name="header" type="select" label="Header in output">
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71 <option value="-h">Include Header</option>
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72 <option value="">Exclude Header</option>
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73 <option value="-H">Only the Header</option>
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74 </param>
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75 <param name="mapq" type="integer" value="" optional="true" label="Minimum MAPQ quality score" help="(-q)">
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76 <validator type="in_range" message="The MAPQ quality score can't be negative" min="0"/>
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77 </param>
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78 <conditional name="flag">
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79 <param name="filter" type="select" label="Filter on bitwise flag">
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80 <option value="no">no</option>
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81 <option value="yes">yes</option>
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82 </param>
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83 <when value="no"/>
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84 <when value="yes">
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85 <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" help="(-f)">
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86 <option value="0x0001">Read is paired</option>
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87 <option value="0x0002">Read is mapped in a proper pair</option>
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88 <option value="0x0004">The read is unmapped</option>
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89 <option value="0x0008">The mate is unmapped</option>
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90 <option value="0x0010">Read strand</option>
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91 <option value="0x0020">Mate strand</option>
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92 <option value="0x0040">Read is the first in a pair</option>
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93 <option value="0x0080">Read is the second in a pair</option>
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94 <option value="0x0100">The alignment or this read is not primary</option>
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95 <option value="0x0200">The read fails platform/vendor quality checks</option>
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96 <option value="0x0400">The read is a PCR or optical duplicate</option>
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97 <option value="0x0800">Supplementary alignment</option>
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98 </param>
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99 <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" help="(-F)">
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100 <option value="0x0001">Read is paired</option>
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101 <option value="0x0002">Read is mapped in a proper pair</option>
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102 <option value="0x0004">The read is unmapped</option>
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103 <option value="0x0008">The mate is unmapped</option>
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104 <option value="0x0010">Read strand</option>
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105 <option value="0x0020">Mate strand</option>
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106 <option value="0x0040">Read is the first in a pair</option>
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107 <option value="0x0080">Read is the second in a pair</option>
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108 <option value="0x0100">The alignment or this read is not primary</option>
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109 <option value="0x0200">The read fails platform/vendor quality checks</option>
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110 <option value="0x0400">The read is a PCR or optical duplicate</option>
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111 <option value="0x0800">Supplementary alignment</option>
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112 </param>
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113 </when>
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114 </conditional>
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115 <param name="library" type="text" value="" label="Select alignments from Library"
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116 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
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117 <param name="read_group" type="text" value="" label="Select alignments from Read Group"
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118 help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
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119 <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/>
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120 <param name="possibly_select_inverse" checked="false" label="Use inverse selection" type="boolean" truevalue="-U" falsevalue="-o" help="Select the opposite of the listed chromosomes" />
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121 <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"
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122 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
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123 <param name="outputtype" type="select" label="Select the output format">
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124 <option value="bam">BAM (-b)</option>
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125 <option value="sam">SAM</option>
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126 </param>
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127 </inputs>
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128 <outputs>
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129 <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}">
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130 <change_format>
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131 <when input="outputtype" value="bam" format="bam" />
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132 </change_format>
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133 </data>
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134 </outputs>
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135 <tests>
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136 <test>
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137 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
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138 <param name="header" value=""/>
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139 <param name="filter" value="yes"/>
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140 <param name="reqBits" value="0x0080"/>
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141 <param name="outputtype" value="sam"/>
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142 <output name="output1">
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143 <assert_contents>
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144 <has_text text="141" />
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145 <not_has_text text="77" />
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146 </assert_contents>
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147 </output>
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148 </test>
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149 <test>
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150 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
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151 <param name="header" value=""/>
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152 <param name="filter" value="no"/>
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153 <param name="read_group" value="rg1"/>
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154 <param name="outputtype" value="sam"/>
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155 <output name="output1">
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156 <assert_contents>
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157 <has_text text="rg1" />
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158 <not_has_text text="rg2" />
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159 </assert_contents>
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160 </output>
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161 </test>
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162 <test>
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163 <param name="input1" value="bam_to_sam_in1.sam" ftype="sam" />
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164 <param name="header" value=""/>
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165 <param name="filter" value="yes"/>
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166 <param name="skipBits" value="0x0008"/>
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167 <param name="mapq" value="250"/>
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168 <param name="outputtype" value="sam"/>
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169 <output name="output1">
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170 <assert_contents>
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171 <has_text text="both_reads_align_clip_marked" />
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172 <not_has_text text="both_reads_present_only_first_aligns" />
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173 </assert_contents>
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174 </output>
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175 </test>
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176 </tests>
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177 <help>
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178 **What it does**
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179
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180 This tool uses the samtools view command in SAMtools_ toolkit to filter a SAM or BAM file on the MAPQ (mapping quality), FLAG bits, Read Group, Library, or region.
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181
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182 **Input**
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183
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184 Input is either a SAM or BAM file.
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185
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186 **Output**
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187
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188 The output file will be SAM or BAM (depending on the chosen option), filtered by the selected options.
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189
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190 **Options**
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191
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192 Filtering by read group or library requires headers in the input SAM or BAM file.
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193
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194 If regions are specified, only alignments overlapping the specified regions will be output. An alignment may be given multiple times if it is overlapping several regions.
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195 A region can be presented, for example, in the following format::
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196
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197 chr2 (the whole chr2)
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198 chr2:1000000 (region starting from 1,000,000bp)
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199 chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points).
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200
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201 Note: The coordinate is 1-based.
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202
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203 Multiple regions may be specified, separated by a space character::
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204
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205 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX
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206
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207
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208
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209 .. _SAMtools: http://www.htslib.org/
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210
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211 </help>
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212 </tool>