Mercurial > repos > devteam > samtool_filter2

annotate samtool_filter2.xml @ 17:3263a2b5d9f0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
author iuc
date Wed, 06 Jun 2018 18:43:15 -0400
parents 160964255888
children a201937caf2e
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17
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 16
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1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8">
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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2 <description>files on FLAG MAPQ RG LN or by region</description>
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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3 <requirements>
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4 <requirement type="package" version="1.8">samtools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 ##set up input files, regions requires input.bam and input.bai
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8 #if $input1.is_of_type('bam')
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9 #set $input = 'input.bam'
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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10 ln -s '$input1' $input &&
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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11 ln -s '$input1.metadata.bam_index' input.bai &&
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12 #elif $input1.is_of_type('sam')
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3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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13 #set $input = 'input.sam'
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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14 ln -s '$input1' $input &&
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15 #end if
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16 samtools view
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17 $possibly_select_inverse '$output1'
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18 $header
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19
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20 #if $input1.is_of_type('sam')
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21 -S
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22 #end if
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23
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24 #if str($outputtype) == 'bam'
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25 -b
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26 #end if
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27
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28 #if str($mapq)
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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29 -q $mapq
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30 #end if
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31 #if $flag.filter == 'yes'
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32 #if str($flag.reqBits) != 'None'
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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33 #set $reqs = str($flag.reqBits).split(',')
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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34 #set $reqFlag = 0
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35 #for $xn in $reqs:
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36 #set $reqFlag += int($xn, 16)
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37 #end for
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38 -f $hex($reqFlag)
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39 #end if
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40 #if str($flag.skipBits) != 'None'
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41 #set $skips = str($flag.skipBits).split(',')
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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42 #set $skipFlag = 0
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43 #for $xn in $skips:
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44 #set $skipFlag += int(xn,16)
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45 #end for
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46 -F $hex($skipFlag)
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47 #end if
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48 #end if
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49 #if str($read_group).strip()
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50 -r '$read_group'
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51 #end if
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52 #if str($library).strip()
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53 -l '$library'
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54 #end if
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55 #if $bed_file
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56 -L '$bed_file'
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57 #end if
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58 $input
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59 #if str($regions).strip() and $input1.is_of_type('bam')
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60 #for region in str($regions).split():
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61 '$region'
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62 #end for
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63 #end if
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64 ]]></command>
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65 <inputs>
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66 <param name="input1" type="data" format="sam,bam" label="SAM or BAM file to filter" />
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67 <param name="header" type="select" label="Header in output">
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68 <option value="-h">Include header</option>
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69 <option value="">Exclude header</option>
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70 <option value="-H">Only the header</option>
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71 </param>
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72 <param name="mapq" type="integer" min="0" value="" optional="true" label="Minimum MAPQ quality score" help="(-q)" />
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73 <conditional name="flag">
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74 <param name="filter" type="select" label="Filter on bitwise flag">
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75 <option value="no">no</option>
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76 <option value="yes">yes</option>
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77 </param>
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78 <when value="no"/>
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79 <when value="yes">
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80 <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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81 <option value="0x0001">Read is paired</option>
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82 <option value="0x0002">Read is mapped in a proper pair</option>
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83 <option value="0x0004">The read is unmapped</option>
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84 <option value="0x0008">The mate is unmapped</option>
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85 <option value="0x0010">Read strand</option>
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86 <option value="0x0020">Mate strand</option>
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87 <option value="0x0040">Read is the first in a pair</option>
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88 <option value="0x0080">Read is the second in a pair</option>
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89 <option value="0x0100">The alignment or this read is not primary</option>
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90 <option value="0x0200">The read fails platform/vendor quality checks</option>
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91 <option value="0x0400">The read is a PCR or optical duplicate</option>
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92 <option value="0x0800">Supplementary alignment</option>
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93 </param>
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94 <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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95 <option value="0x0001">Read is paired</option>
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96 <option value="0x0002">Read is mapped in a proper pair</option>
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97 <option value="0x0004">The read is unmapped</option>
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98 <option value="0x0008">The mate is unmapped</option>
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99 <option value="0x0010">Read strand</option>
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100 <option value="0x0020">Mate strand</option>
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101 <option value="0x0040">Read is the first in a pair</option>
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102 <option value="0x0080">Read is the second in a pair</option>
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103 <option value="0x0100">The alignment or this read is not primary</option>
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104 <option value="0x0200">The read fails platform/vendor quality checks</option>
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105 <option value="0x0400">The read is a PCR or optical duplicate</option>
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106 <option value="0x0800">Supplementary alignment</option>
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107 </param>
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108 </when>
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109 </conditional>
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110 <param name="library" type="text" value="" label="Select alignments from Library"
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111 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
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112 <param name="read_group" type="text" value="" label="Select alignments from Read Group"
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113 help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
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114 <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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115 <param name="possibly_select_inverse" type="boolean" truevalue="-U" falsevalue="-o" checked="false" label="Use inverse selection" help="Select the opposite of the listed chromosomes" />
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116 <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"
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117 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
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118 <param name="outputtype" type="select" label="Select the output format">
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119 <option value="bam">BAM (-b)</option>
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120 <option value="sam">SAM</option>
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121 </param>
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122 </inputs>
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123 <outputs>
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124 <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}">
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125 <change_format>
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126 <when input="outputtype" value="bam" format="bam" />
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127 </change_format>
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128 </data>
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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="input1" value="bam_to_sam_in2.sam" ftype="sam" />
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133 <param name="header" value=""/>
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134 <param name="filter" value="yes"/>
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135 <param name="reqBits" value="0x0080"/>
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136 <param name="outputtype" value="sam"/>
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137 <output name="output1">
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138 <assert_contents>
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139 <has_text text="141" />
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140 <not_has_text text="77" />
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141 </assert_contents>
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142 </output>
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143 </test>
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144 <test>
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145 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
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146 <param name="header" value=""/>
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147 <param name="filter" value="no"/>
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148 <param name="read_group" value="rg1"/>
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149 <param name="outputtype" value="sam"/>
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150 <output name="output1">
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151 <assert_contents>
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152 <has_text text="rg1" />
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153 <not_has_text text="rg2" />
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154 </assert_contents>
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155 </output>
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156 </test>
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157 <test>
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158 <param name="input1" value="bam_to_sam_in1.sam" ftype="sam" />
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159 <param name="header" value=""/>
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160 <param name="filter" value="yes"/>
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161 <param name="skipBits" value="0x0008"/>
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162 <param name="mapq" value="250"/>
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163 <param name="outputtype" value="sam"/>
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164 <output name="output1">
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165 <assert_contents>
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166 <has_text text="both_reads_align_clip_marked" />
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167 <not_has_text text="both_reads_present_only_first_aligns" />
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168 </assert_contents>
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169 </output>
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170 </test>
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171 </tests>
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172 <help><![CDATA[
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173 **What it does**
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174
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175 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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176
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177 **Input**
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178
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179 Input is either a SAM or BAM file.
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180
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181 **Output**
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182
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183 The output file will be SAM or BAM (depending on the chosen option), filtered by the selected options.
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184
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185 **Options**
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186
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187 Filtering by read group or library requires headers in the input SAM or BAM file.
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188
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189 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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190 A region can be presented, for example, in the following format::
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191
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192 chr2 (the whole chr2)
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193 chr2:1000000 (region starting from 1,000,000bp)
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194 chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points).
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195
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196 Note: The coordinate is 1-based.
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197
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198 Multiple regions may be specified, separated by a space character::
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199
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200 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX
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201
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202 .. _SAMtools: http://www.htslib.org/
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203 ]]></help>
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204 <citations>
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205 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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206 </citations>
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207 </tool>