Mercurial > repos > devteam > samtool_filter2
annotate samtool_filter2.xml @ 10:5596f413349f draft
Uploaded new version from GH
| author | devteam |
|---|---|
| date | Mon, 10 Nov 2014 16:57:03 -0500 |
| parents | ce2ed9f2d811 |
| children | a2b5298e7239 |
| rev | line source |
|---|---|
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ce2ed9f2d811
added test data from samtools_filter, renamed xml file, fixed tests, changed changeset revision of dependency
Dorine <dorine@bx.psu.edu>
parents:
8
diff
changeset
|
1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.1"> |
| 7 | 2 <description>files on FLAG MAPQ RG LN or by region</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.1.18">samtools</requirement> | |
| 5 </requirements> | |
| 6 <!-- | |
| 7 samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] <in.bam>|<in.sam> [region1 [...]] | |
| 8 Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]] | |
| 9 | |
| 10 Options: -b output BAM | |
| 11 -h print header for the SAM output | |
| 12 -H print header only (no alignments) | |
| 13 -S input is SAM | |
| 14 -u uncompressed BAM output (force -b) | |
| 15 -1 fast compression (force -b) | |
| 16 -x output FLAG in HEX (samtools-C specific) | |
| 17 -X output FLAG in string (samtools-C specific) | |
| 18 -c print only the count of matching records | |
| 19 -L FILE output alignments overlapping the input BED FILE [null] | |
| 20 -t FILE list of reference names and lengths (force -S) [null] | |
| 21 -T FILE reference sequence file (force -S) [null] | |
| 22 -o FILE output file name [stdout] | |
| 23 -R FILE list of read groups to be outputted [null] | |
| 24 -f INT required flag, 0 for unset [0] | |
| 25 -F INT filtering flag, 0 for unset [0] | |
| 26 -q INT minimum mapping quality [0] | |
| 27 -l STR only output reads in library STR [null] | |
| 28 -r STR only output reads in read group STR [null] | |
| 29 -? longer help | |
| 30 --> | |
| 31 <command> | |
| 32 ##set up input files, regions requires input.bam and input.bai | |
| 33 #if isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('bam').__class__): | |
| 34 #set $input = 'input.bam' | |
| 35 ln -s $input1 $input && | |
| 36 ln -s $input1.metadata.bam_index input.bai && | |
| 37 #elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sam').__class__): | |
| 38 #set $input = 'input.sam' | |
| 39 ln -s $input1 $input && | |
| 40 #end if | |
| 41 samtools view -o "$output1" $header | |
| 42 | |
| 43 #if $input1.datatype.file_ext == 'sam': | |
| 44 -S | |
| 45 #end if | |
| 46 | |
| 47 #if $outputtype.__str__ == "bam": | |
| 48 -b | |
| 49 #end if | |
| 50 | |
| 51 | |
| 52 #if $mapq.__str__ != '': | |
| 53 -q $mapq | |
| 54 #end if | |
| 55 #if $flag.filter.__str__ == 'yes': | |
| 56 #if $flag.reqBits.__str__ != 'None': | |
| 57 #set $reqs = $flag.reqBits.__str__.split(',') | |
| 58 #set $reqFlag = 0 | |
| 59 #for $xn in $reqs: | |
| 60 #set $reqFlag += int(xn,16) | |
| 61 #end for | |
| 62 -f $hex($reqFlag) | |
| 63 #end if | |
| 64 #if $flag.skipBits.__str__ != 'None': | |
| 65 #set $skips = $flag.skipBits.__str__.split(',') | |
| 66 #set $skipFlag = 0 | |
| 67 #for $xn in $skips: | |
| 68 #set $skipFlag += int(xn,16) | |
| 69 #end for | |
| 70 -F $hex($skipFlag) | |
| 71 #end if | |
| 72 #end if | |
| 73 #if $read_group.__str__.strip() != '': | |
| 74 -r $read_group | |
| 75 #end if | |
| 76 #if $library.__str__.strip() != '': | |
| 77 -l $library | |
| 78 #end if | |
| 79 #if $bed_file.__str__ != "None" and len($bed_file.__str__) > 0: | |
| 80 -L $bed_file | |
| 81 #end if | |
| 82 $input | |
| 83 #if $regions.__str__.strip() != '' and $input1.datatype.file_ext == 'bam': | |
| 84 $regions.__str__.strip() | |
| 85 #end if | |
| 86 ## need to redirect stderr message so galaxy does not think this failed | |
| 87 2>&1 | |
| 88 </command> | |
| 89 <inputs> | |
| 90 <param name="input1" type="data" format="sam,bam" label="SAM or BAM File to Filter" /> | |
| 91 <param name="header" type="select" label="Header in output"> | |
| 92 <option value="-h">Include Header</option> | |
| 93 <option value="">Exclude Header</option> | |
| 94 <option value="-H">Only the Header</option> | |
| 95 </param> | |
| 96 <param name="mapq" type="integer" value="" optional="true" label="Minimum MAPQ quality score"> | |
| 97 <validator type="in_range" message="The MAPQ quality score can't be negative" min="0"/> | |
| 98 </param> | |
| 99 <conditional name="flag"> | |
| 100 <param name="filter" type="select" label="Filter on bitwise flag"> | |
| 101 <option value="no">no</option> | |
| 102 <option value="yes">yes</option> | |
| 103 </param> | |
| 104 <when value="no"/> | |
| 105 <when value="yes"> | |
| 106 <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" > | |
| 107 <option value="0x0001">Read is paired</option> | |
| 108 <option value="0x0002">Read is mapped in a proper pair</option> | |
| 109 <option value="0x0004">The read is unmapped</option> | |
| 110 <option value="0x0008">The mate is unmapped</option> | |
| 111 <option value="0x0010">Read strand</option> | |
| 112 <option value="0x0020">Mate strand</option> | |
| 113 <option value="0x0040">Read is the first in a pair</option> | |
| 114 <option value="0x0080">Read is the second in a pair</option> | |
| 115 <option value="0x0100">The alignment or this read is not primary</option> | |
| 116 <option value="0x0200">The read fails platform/vendor quality checks</option> | |
| 117 <option value="0x0400">The read is a PCR or optical duplicate</option> | |
| 118 </param> | |
| 119 <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" > | |
| 120 <option value="0x0001">Read is paired</option> | |
| 121 <option value="0x0002">Read is mapped in a proper pair</option> | |
| 122 <option value="0x0004">The read is unmapped</option> | |
| 123 <option value="0x0008">The mate is unmapped</option> | |
| 124 <option value="0x0010">Read strand</option> | |
| 125 <option value="0x0020">Mate strand</option> | |
| 126 <option value="0x0040">Read is the first in a pair</option> | |
| 127 <option value="0x0080">Read is the second in a pair</option> | |
| 128 <option value="0x0100">The alignment or this read is not primary</option> | |
| 129 <option value="0x0200">The read fails platform/vendor quality checks</option> | |
| 130 <option value="0x0400">The read is a PCR or optical duplicate</option> | |
| 131 </param> | |
| 132 </when> | |
| 133 </conditional> | |
| 134 <param name="library" type="text" value="" size="20" label="Select alignments from Library" | |
| 135 help="Requires headers in the input SAM or BAM, otherwise no alignments will be output."/> | |
| 136 <param name="read_group" type="text" value="" size="20" label="Select alignments from Read Group" | |
| 137 help="Requires headers in the input SAM or BAM, otherwise no alignments will be output."/> | |
| 138 <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE"/> | |
| 139 <param name="regions" type="text" value="" size="180" label="Select regions (only used when the input is in BAM format)" | |
| 140 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/> | |
| 141 <param name="outputtype" type="select" label="Select the output format"> | |
| 142 <option value="bam">bam</option> | |
| 143 <option value="sam">sam</option> | |
| 144 </param> | |
| 145 </inputs> | |
| 146 <outputs> | |
|
9
ce2ed9f2d811
added test data from samtools_filter, renamed xml file, fixed tests, changed changeset revision of dependency
Dorine <dorine@bx.psu.edu>
parents:
8
diff
changeset
|
147 <data name="output1" format_source="input1" label="${tool.name} on ${on_string}: ${input1.datatype.file_ext}"> |
|
ce2ed9f2d811
added test data from samtools_filter, renamed xml file, fixed tests, changed changeset revision of dependency
Dorine <dorine@bx.psu.edu>
parents:
8
diff
changeset
|
148 <change_format> |
|
ce2ed9f2d811
added test data from samtools_filter, renamed xml file, fixed tests, changed changeset revision of dependency
Dorine <dorine@bx.psu.edu>
parents:
8
diff
changeset
|
149 <when input="outputtype" value="bam" format="bam" /> |
| 10 | 150 <when input="outputtype" value="sam" format="sam" /> |
| 7 | 151 </change_format> |
| 152 </data> | |
| 153 </outputs> | |
| 154 <tests> | |
| 155 <test> | |
| 156 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" /> | |
| 157 <param name="header" value=""/> | |
| 158 <param name="filter" value="yes"/> | |
| 159 <param name="reqBits" value="0x0080"/> | |
|
9
ce2ed9f2d811
added test data from samtools_filter, renamed xml file, fixed tests, changed changeset revision of dependency
Dorine <dorine@bx.psu.edu>
parents:
8
diff
changeset
|
160 <param name="outputtype" value="sam"/> |
| 7 | 161 <output name="output1" > |
| 162 <assert_contents> | |
| 163 <has_text text="141" /> | |
| 164 <not_has_text text="77" /> | |
| 165 </assert_contents> | |
| 166 </output> | |
| 167 </test> | |
| 168 <test> | |
| 169 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" /> | |
| 170 <param name="header" value=""/> | |
| 171 <param name="filter" value="no"/> | |
| 172 <param name="read_group" value="rg1"/> | |
|
9
ce2ed9f2d811
added test data from samtools_filter, renamed xml file, fixed tests, changed changeset revision of dependency
Dorine <dorine@bx.psu.edu>
parents:
8
diff
changeset
|
173 <param name="outputtype" value="sam"/> |
| 7 | 174 <output name="output1" > |
| 175 <assert_contents> | |
| 176 <has_text text="rg1" /> | |
| 177 <not_has_text text="rg2" /> | |
| 178 </assert_contents> | |
| 179 </output> | |
| 180 </test> | |
| 181 <test> | |
| 182 <param name="input1" value="bam_to_sam_in1.sam" ftype="sam" /> | |
| 183 <param name="header" value=""/> | |
| 184 <param name="filter" value="yes"/> | |
| 185 <param name="skipBits" value="0x0008"/> | |
| 186 <param name="mapq" value="250"/> | |
|
9
ce2ed9f2d811
added test data from samtools_filter, renamed xml file, fixed tests, changed changeset revision of dependency
Dorine <dorine@bx.psu.edu>
parents:
8
diff
changeset
|
187 <param name="outputtype" value="sam"/> |
| 7 | 188 <output name="output1" > |
| 189 <assert_contents> | |
| 190 <has_text text="both_reads_align_clip_marked" /> | |
| 191 <not_has_text text="both_reads_present_only_first_aligns" /> | |
| 192 </assert_contents> | |
| 193 </output> | |
| 194 </test> | |
| 195 </tests> | |
| 196 <help> | |
| 197 | |
| 198 | |
| 199 **What it does** | |
| 200 | |
| 201 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. | |
| 202 | |
| 203 **Input** | |
| 204 | |
| 205 Input is either a SAM or BAM file. | |
| 206 | |
| 207 **Output** | |
| 208 | |
| 209 The output file will be SAM or BAM (depending on the chosen option), filtered by the selected options. | |
| 210 | |
| 211 **Options** | |
| 212 | |
| 213 Filtering by read group or library requires headers in the input SAM or BAM file. | |
| 214 | |
| 215 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. | |
| 216 A region can be presented, for example, in the following format:: | |
| 217 | |
| 218 chr2 (the whole chr2) | |
| 219 chr2:1000000 (region starting from 1,000,000bp) | |
| 220 chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points). | |
| 221 | |
| 222 Note: The coordinate is 1-based. | |
| 223 | |
| 224 Multiple regions may be specified, separated by a space character:: | |
| 225 | |
| 226 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX | |
| 227 | |
| 228 | |
| 229 | |
| 230 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml | |
| 231 | |
| 232 </help> | |
| 233 </tool> |