Mercurial > repos > devteam > samtool_filter2

annotate samtool_filter2.xml @ 18:a201937caf2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
author iuc
date Wed, 31 Jul 2019 14:19:38 -0400
parents 3263a2b5d9f0
children
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18
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
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1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8+galaxy1">
17
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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
iuc
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3 <requirements>
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
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4 <requirement type="package" version="1.8">samtools</requirement>
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
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5 </requirements>
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a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
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6 <macros>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
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7 <xml name="flag_options">
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
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8 <option value="0x0001">Read is paired</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
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9 <option value="0x0002">Read is mapped in a proper pair</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
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10 <option value="0x0004">The read is unmapped</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
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11 <option value="0x0008">The mate is unmapped</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
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12 <option value="0x0010">Read is mapped to the reverse strand of the reference</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
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13 <option value="0x0020">Mate is mapped to the reverse strand of the reference</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
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14 <option value="0x0040">Read is the first in a pair</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
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15 <option value="0x0080">Read is the second in a pair</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
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16 <option value="0x0100">The alignment of this read is not primary</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
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17 <option value="0x0200">The read fails platform/vendor quality checks</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
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18 <option value="0x0400">The read is a PCR or optical duplicate</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
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19 <option value="0x0800">Supplementary alignment</option>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
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20 </xml>
a201937caf2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
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21 </macros>
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22 <command detect_errors="exit_code"><![CDATA[
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23 ##set up input files, regions requires input.bam and input.bai
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24 #if $input1.is_of_type('bam')
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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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25 #set $input = 'input.bam'
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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26 ln -s '$input1' $input &&
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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27 ln -s '$input1.metadata.bam_index' input.bai &&
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28 #elif $input1.is_of_type('sam')
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29 #set $input = 'input.sam'
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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30 ln -s '$input1' $input &&
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31 #end if
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32 samtools view
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33 $possibly_select_inverse '$output1'
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34 $header
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35
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36 #if $input1.is_of_type('sam')
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37 -S
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38 #end if
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39
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40 #if str($outputtype) == 'bam'
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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41 -b
3263a2b5d9f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
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42 #end if
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43
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44 #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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45 -q $mapq
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46 #end if
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47 #if $flag.filter == 'yes'
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48 #if str($flag.reqBits) != 'None'
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49 #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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50 #set $reqFlag = 0
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51 #for $xn in $reqs:
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52 #set $reqFlag += int($xn, 16)
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53 #end for
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54 -f $hex($reqFlag)
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55 #end if
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56 #if str($flag.skipBits) != 'None'
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57 #set $skips = str($flag.skipBits).split(',')
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58 #set $skipFlag = 0
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59 #for $xn in $skips:
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60 #set $skipFlag += int(xn,16)
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61 #end for
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62 -F $hex($skipFlag)
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63 #end if
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64 #end if
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65 #if str($read_group).strip()
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66 -r '$read_group'
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67 #end if
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68 #if str($library).strip()
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69 -l '$library'
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70 #end if
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71 #if $bed_file
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72 -L '$bed_file'
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73 #end if
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74 $input
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75 #if str($regions).strip() and $input1.is_of_type('bam')
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76 #for region in str($regions).split():
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77 '$region'
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78 #end for
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79 #end if
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80 ]]></command>
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81 <inputs>
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82 <param name="input1" type="data" format="sam,bam" label="SAM or BAM file to filter" />
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83 <param name="header" type="select" label="Header in output">
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84 <option value="-h">Include header</option>
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85 <option value="">Exclude header</option>
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86 <option value="-H">Only the header</option>
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87 </param>
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88 <param name="mapq" type="integer" min="0" value="" optional="true" label="Minimum MAPQ quality score" help="(-q)" />
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89 <conditional name="flag">
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90 <param name="filter" type="select" label="Filter on bitwise flag">
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91 <option value="no">no</option>
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92 <option value="yes">yes</option>
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93 </param>
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94 <when value="no"/>
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95 <when value="yes">
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96 <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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97 <expand macro="flag_options" />
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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 <expand macro="flag_options" />
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101 </param>
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102 </when>
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103 </conditional>
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104 <param name="library" type="text" value="" label="Select alignments from Library"
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105 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
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106 <param name="read_group" type="text" value="" label="Select alignments from Read Group"
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107 help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
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108 <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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109 <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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110 <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"
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111 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
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112 <param name="outputtype" type="select" label="Select the output format">
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113 <option value="bam">BAM (-b)</option>
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114 <option value="sam">SAM</option>
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115 </param>
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116 </inputs>
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117 <outputs>
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118 <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}">
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119 <change_format>
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120 <when input="outputtype" value="bam" format="bam" />
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121 </change_format>
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122 </data>
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123 </outputs>
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124 <tests>
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125 <test>
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126 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
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127 <param name="header" value=""/>
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128 <param name="filter" value="yes"/>
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129 <param name="reqBits" value="0x0080"/>
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130 <param name="outputtype" value="sam"/>
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131 <output name="output1">
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132 <assert_contents>
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133 <has_text text="141" />
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134 <not_has_text text="77" />
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135 </assert_contents>
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136 </output>
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137 </test>
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138 <test>
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139 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
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140 <param name="header" value=""/>
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141 <param name="filter" value="no"/>
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142 <param name="read_group" value="rg1"/>
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143 <param name="outputtype" value="sam"/>
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144 <output name="output1">
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145 <assert_contents>
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146 <has_text text="rg1" />
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147 <not_has_text text="rg2" />
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148 </assert_contents>
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149 </output>
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150 </test>
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151 <test>
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152 <param name="input1" value="bam_to_sam_in1.sam" ftype="sam" />
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153 <param name="header" value=""/>
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154 <param name="filter" value="yes"/>
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155 <param name="skipBits" value="0x0008"/>
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156 <param name="mapq" value="250"/>
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157 <param name="outputtype" value="sam"/>
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158 <output name="output1">
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159 <assert_contents>
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160 <has_text text="both_reads_align_clip_marked" />
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161 <not_has_text text="both_reads_present_only_first_aligns" />
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162 </assert_contents>
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163 </output>
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164 </test>
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165 </tests>
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166 <help><![CDATA[
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167 **What it does**
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168
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169 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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170
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171 **Input**
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172
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173 Input is either a SAM or BAM file.
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174
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175 **Output**
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176
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177 The output file will be SAM or BAM (depending on the chosen option), filtered by the selected options.
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178
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179 **Options**
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180
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181 Filtering by read group or library requires headers in the input SAM or BAM file.
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182
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183 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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184 A region can be presented, for example, in the following format::
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185
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186 chr2 (the whole chr2)
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187 chr2:1000000 (region starting from 1,000,000bp)
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188 chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points).
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189
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190 Note: The coordinate is 1-based.
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191
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192 Multiple regions may be specified, separated by a space character::
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193
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194 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX
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195
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196 .. _SAMtools: http://www.htslib.org/
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197 ]]></help>
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198 <citations>
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199 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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200 </citations>
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201 </tool>