Mercurial > repos > devteam > samtool_filter2
annotate samtool_filter2.xml @ 16:160964255888 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit a97efd3ee05c6e27ff8294f66ea975445966d9c4
author | devteam |
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date | Thu, 05 Oct 2017 10:31:25 -0400 |
parents | 1ea3b8a4c2fe |
children | 3263a2b5d9f0 |
rev | line source |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit d02925461fc5d6188099a60c1996c671a0bde828
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1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.2"> |
7 | 2 <description>files on FLAG MAPQ RG LN or by region</description> |
3 <requirements> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit d02925461fc5d6188099a60c1996c671a0bde828
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4 <requirement type="package" version="1.2">samtools</requirement> |
7 | 5 </requirements> |
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6 <stdio> |
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7 <exit_code range="1:" /> |
543405859e60
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8 </stdio> |
7 | 9 <command> |
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10 <![CDATA[ |
7 | 11 ##set up input files, regions requires input.bam and input.bai |
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1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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12 #if $input1.is_of_type('bam') |
7 | 13 #set $input = 'input.bam' |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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14 ln -s '$input1' $input && |
1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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15 ln -s '$input1.metadata.bam_index' input.bai && |
1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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16 #elif $input1.is_of_type('sam') |
7 | 17 #set $input = 'input.sam' |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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18 ln -s '$input1' $input && |
7 | 19 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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20 samtools view $possibly_select_inverse '$output1' $header |
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21 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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22 #if $input1.is_of_type('sam') |
7 | 23 -S |
24 #end if | |
25 | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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26 #if str($outputtype) == 'bam' |
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27 -b |
7 | 28 #end if |
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29 |
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1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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30 #if str($mapq) |
7 | 31 -q $mapq |
32 #end if | |
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1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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33 #if $flag.filter == 'yes' |
1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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34 #if str($flag.reqBits) != 'None' |
1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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35 #set $reqs = str($flag.reqBits).split(',') |
7 | 36 #set $reqFlag = 0 |
37 #for $xn in $reqs: | |
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1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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38 #set $reqFlag += int($xn, 16) |
7 | 39 #end for |
40 -f $hex($reqFlag) | |
41 #end if | |
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1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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42 #if str($flag.skipBits) != 'None' |
1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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43 #set $skips = str($flag.skipBits).split(',') |
7 | 44 #set $skipFlag = 0 |
45 #for $xn in $skips: | |
46 #set $skipFlag += int(xn,16) | |
47 #end for | |
48 -F $hex($skipFlag) | |
49 #end if | |
50 #end if | |
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1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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51 #if str($read_group).strip() |
1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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52 -r '$read_group' |
7 | 53 #end if |
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1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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54 #if str($library).strip() |
1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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55 -l '$library' |
7 | 56 #end if |
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1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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57 #if $bed_file |
1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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58 -L '$bed_file' |
7 | 59 #end if |
60 $input | |
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1ea3b8a4c2fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
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61 #if str($regions).strip() and $input1.is_of_type('bam') |
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160964255888
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit a97efd3ee05c6e27ff8294f66ea975445966d9c4
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62 #for region in str($regions).split(): |
160964255888
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit a97efd3ee05c6e27ff8294f66ea975445966d9c4
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63 '$region' |
160964255888
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit a97efd3ee05c6e27ff8294f66ea975445966d9c4
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64 #end for |
7 | 65 #end if |
66 ## need to redirect stderr message so galaxy does not think this failed | |
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67 2>&1 |
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68 ]]> |
7 | 69 </command> |
70 <inputs> | |
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71 <param name="input1" type="data" format="sam,bam" label="SAM or BAM file to filter" /> |
7 | 72 <param name="header" type="select" label="Header in output"> |
73 <option value="-h">Include Header</option> | |
74 <option value="">Exclude Header</option> | |
75 <option value="-H">Only the Header</option> | |
76 </param> | |
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77 <param name="mapq" type="integer" value="" optional="true" label="Minimum MAPQ quality score" help="(-q)"> |
7 | 78 <validator type="in_range" message="The MAPQ quality score can't be negative" min="0"/> |
79 </param> | |
80 <conditional name="flag"> | |
81 <param name="filter" type="select" label="Filter on bitwise flag"> | |
82 <option value="no">no</option> | |
83 <option value="yes">yes</option> | |
84 </param> | |
85 <when value="no"/> | |
86 <when value="yes"> | |
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87 <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" help="(-f)"> |
7 | 88 <option value="0x0001">Read is paired</option> |
89 <option value="0x0002">Read is mapped in a proper pair</option> | |
90 <option value="0x0004">The read is unmapped</option> | |
91 <option value="0x0008">The mate is unmapped</option> | |
92 <option value="0x0010">Read strand</option> | |
93 <option value="0x0020">Mate strand</option> | |
94 <option value="0x0040">Read is the first in a pair</option> | |
95 <option value="0x0080">Read is the second in a pair</option> | |
96 <option value="0x0100">The alignment or this read is not primary</option> | |
97 <option value="0x0200">The read fails platform/vendor quality checks</option> | |
98 <option value="0x0400">The read is a PCR or optical duplicate</option> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 47865f133813c9e61ffc63d70aad1ff782c645ac
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99 <option value="0x0800">Supplementary alignment</option> |
7 | 100 </param> |
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101 <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" help="(-F)"> |
7 | 102 <option value="0x0001">Read is paired</option> |
103 <option value="0x0002">Read is mapped in a proper pair</option> | |
104 <option value="0x0004">The read is unmapped</option> | |
105 <option value="0x0008">The mate is unmapped</option> | |
106 <option value="0x0010">Read strand</option> | |
107 <option value="0x0020">Mate strand</option> | |
108 <option value="0x0040">Read is the first in a pair</option> | |
109 <option value="0x0080">Read is the second in a pair</option> | |
110 <option value="0x0100">The alignment or this read is not primary</option> | |
111 <option value="0x0200">The read fails platform/vendor quality checks</option> | |
112 <option value="0x0400">The read is a PCR or optical duplicate</option> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 47865f133813c9e61ffc63d70aad1ff782c645ac
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113 <option value="0x0800">Supplementary alignment</option> |
7 | 114 </param> |
115 </when> | |
116 </conditional> | |
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117 <param name="library" type="text" value="" label="Select alignments from Library" |
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118 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/> |
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119 <param name="read_group" type="text" value="" label="Select alignments from Read Group" |
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120 help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/> |
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121 <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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122 <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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123 <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)" |
7 | 124 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/> |
125 <param name="outputtype" type="select" label="Select the output format"> | |
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126 <option value="bam">BAM (-b)</option> |
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127 <option value="sam">SAM</option> |
7 | 128 </param> |
129 </inputs> | |
130 <outputs> | |
11 | 131 <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}"> |
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132 <change_format> |
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133 <when input="outputtype" value="bam" format="bam" /> |
7 | 134 </change_format> |
135 </data> | |
136 </outputs> | |
137 <tests> | |
138 <test> | |
139 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" /> | |
140 <param name="header" value=""/> | |
141 <param name="filter" value="yes"/> | |
142 <param name="reqBits" value="0x0080"/> | |
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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="141" /> |
7 | 147 <not_has_text text="77" /> |
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148 </assert_contents> |
7 | 149 </output> |
150 </test> | |
151 <test> | |
152 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" /> | |
153 <param name="header" value=""/> | |
154 <param name="filter" value="no"/> | |
155 <param name="read_group" value="rg1"/> | |
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156 <param name="outputtype" value="sam"/> |
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157 <output name="output1"> |
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158 <assert_contents> |
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159 <has_text text="rg1" /> |
7 | 160 <not_has_text text="rg2" /> |
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161 </assert_contents> |
7 | 162 </output> |
163 </test> | |
164 <test> | |
165 <param name="input1" value="bam_to_sam_in1.sam" ftype="sam" /> | |
166 <param name="header" value=""/> | |
167 <param name="filter" value="yes"/> | |
168 <param name="skipBits" value="0x0008"/> | |
169 <param name="mapq" value="250"/> | |
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170 <param name="outputtype" value="sam"/> |
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171 <output name="output1"> |
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172 <assert_contents> |
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173 <has_text text="both_reads_align_clip_marked" /> |
7 | 174 <not_has_text text="both_reads_present_only_first_aligns" /> |
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175 </assert_contents> |
7 | 176 </output> |
177 </test> | |
178 </tests> | |
179 <help> | |
180 **What it does** | |
181 | |
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182 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. |
7 | 183 |
184 **Input** | |
185 | |
186 Input is either a SAM or BAM file. | |
187 | |
188 **Output** | |
189 | |
190 The output file will be SAM or BAM (depending on the chosen option), filtered by the selected options. | |
191 | |
192 **Options** | |
193 | |
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194 Filtering by read group or library requires headers in the input SAM or BAM file. |
7 | 195 |
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196 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. |
7 | 197 A region can be presented, for example, in the following format:: |
198 | |
199 chr2 (the whole chr2) | |
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200 chr2:1000000 (region starting from 1,000,000bp) |
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201 chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points). |
7 | 202 |
203 Note: The coordinate is 1-based. | |
204 | |
205 Multiple regions may be specified, separated by a space character:: | |
206 | |
207 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX | |
208 | |
209 | |
210 | |
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211 .. _SAMtools: http://www.htslib.org/ |
7 | 212 |
213 </help> | |
214 </tool> |