Mercurial > repos > miller-lab > genome_diversity
annotate extract_flanking_dna.xml @ 9:22fe0154fa54
added support for heterochromatic regions
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Tue, 10 Jul 2012 11:41:22 -0400 |
| parents | e29f4d801bb0 |
| children | 9b92372de9f6 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gd_extract_flanking_dna" name="Extract" version="1.0.0"> |
| 2 <description>DNA flanking chosen SNPs</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 extract_flanking_dna.py "--input=$input" "--output=$output" "--snps_loc=${GALAXY_DATA_INDEX_DIR}/gd.snps.loc" | |
| 6 #if $override_metadata.choice == "0": | |
| 7 "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}" | |
| 8 #else | |
| 9 "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species" | |
| 10 #end if | |
| 11 "--output_format=$output_format" | |
| 12 </command> | |
| 13 | |
| 14 <inputs> | |
| 15 <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/> | |
| 16 <param name="output_format" type="select" format="integer" label="output format"> | |
| 17 <option value="fasta" selected="true">FastA format</option> | |
| 18 <option value="primer3">Primer3 input</option> | |
| 19 </param> | |
| 20 <conditional name="override_metadata"> | |
| 21 <param name="choice" type="select" format="integer" label="choose columns"> | |
| 22 <option value="0" selected="true">No, get columns from metadata</option> | |
| 23 <option value="1" >Yes, choose columns</option> | |
| 24 </param> | |
| 25 <when value="0" /> | |
| 26 <when value="1"> | |
| 27 <param name="scaf_col" type="data_column" data_ref="input" numerical="false" label="Column with scaffold"/> | |
| 28 <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/> | |
| 29 <param name="species" type="select" label="Choose species"> | |
| 30 <options from_file="gd.species.txt"> | |
| 31 <column name="name" index="1"/> | |
| 32 <column name="value" index="0"/> | |
| 33 </options> | |
| 34 </param> | |
| 35 </when> | |
| 36 </conditional> | |
| 37 </inputs> | |
| 38 | |
| 39 <outputs> | |
| 40 <data format="txt" name="output"/> | |
| 41 </outputs> | |
| 42 | |
| 43 <!-- Need snpcalls files from Webb before uncommenting | |
| 44 <tests> | |
| 45 <test> | |
|
7
e29f4d801bb0
change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
46 <param name="input" value="test_out/select_snps/select_snps.snp" ftype="snp" /> |
| 0 | 47 <param name="output_format" value="primer3" /> |
| 48 <param name="choice" value="0" /> | |
| 49 <output name="output" file="test_out/extract_flanking_dna/extract_flanking_dna.txt" /> | |
| 50 </test> | |
| 51 </tests> | |
| 52 --> | |
| 53 | |
| 54 <help> | |
| 55 **What it does** | |
| 56 | |
| 57 It reports a DNA segment containing each SNP, with up to 200 nucleotides on | |
| 58 either side of the SNP position, which is indicated by "n". Fewer nucleotides | |
| 59 are reported if the SNP is near an end of the assembled genome fragment. | |
| 60 | |
| 61 ----- | |
| 62 | |
| 63 **Example** | |
| 64 | |
| 65 - input file:: | |
| 66 | |
| 67 chr2_75111355_75112576 314 A C L F chr2 75111676 C F 15 4 53 2 9 48 Y 96 0.369 0.355 0.396 0 | |
| 68 chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2 | |
| 69 chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0 | |
| 70 chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1 | |
| 71 chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0 | |
| 72 chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0 | |
| 73 chr18_50154905_50155664 304 A G Y C chr18 50155208 A Y 4 2 17 5 1 22 Y 8 0.022 0.996 0.128 0 | |
| 74 chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1 | |
| 75 chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0 | |
| 76 chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4 | |
| 77 etc. | |
| 78 | |
| 79 - output file:: | |
| 80 | |
| 81 > chr2_75111355_75112576 314 A C | |
| 82 TATCTTCATTTTTATTATAGACTCTCTGAACCAATTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGCAAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAACAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACATGATCAGGGGCAAGTTCTATTGGATATAGTCTTCAAGCATCTTGATTTGACTGAGCGTGACTATTTTGGTTTGCAGTTGACTGACGATTCCACTGATAACCCAGTAAGTTTAAGCTGTTGTCTTTCATTGTCATTGCAATTTTTCTGTCTTTATACTAGGTCCTTTCTGATTTACATTGTTCACTGATT | |
| 83 > chr8_93901796_93905612 2471 A C | |
| 84 GCTGCCGCTGGATTTACTTCTGCTTGGGTCGAGAGCGGGCTGGATGGGTGAAGAGTGGGCTCCCCGGCCCCTGACCAGGCAGGTGCAGACAAGTCGGAAGAAGGCCCGCCGCATCTCCTTGCTGGCCAGCGTGTAGATGACGGGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATnGCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAGCAGGCGATGAACACGCTCACCACGATCACCACGGTCCGCAGCAGGGCCATGGACCGCTCTGAGTTGTGCGGGCTGGCCACCCTGCGGCTGCTGGACTTCACCAGGAAGTAGATGCGTGCGTACAGGATCACGATGGTCAC | |
| 85 > chr10_7434473_7435447 524 T C | |
| 86 ATTATTAACAGAAACATTTCTTTTTCATTACCCAGGGGTTACACTGGTCGTTGATGTTAATCAGTTTTTGGAGAAGGAGAAGCAAAGTGATATTTTGTCTGTTCTGAAGCCTGCCGTTGGTAATACAAATGACGTAATCCCTGAATGTGCTGACAGGTACCATGACGCCCTGGCAAAAGCAAAAGAGCAAAAATCTAGAAGnGGTAAGCATCTTCACTGTTTAGCACAAATTAAATAGCACTTTGAATATGATGATTTCTGTGGTATTGTGTTATCTTACTTTTGAGACAAATAATCGCTTTCAAATGAATATTTCTGAATGTTTGTCATCTCTGGCAAGGAAATTTTTTAGTGTTTCTTTTCCTTTTTTGTCTTTTGGAAATCTGTGATTAACTTGGTGGC | |
| 87 > chr14_80021455_80022064 138 G A | |
| 88 ACCCAGGGATCAAACCCAGGTCTCCCGCATTGCAGGCGGATTCTTTACTGTCTGAGCCTCCAGGGAAGCCCTCGGGGCTGAAGGGATGGTTATGAAGGTGAGAAACAGGGGCCACCTGTCCCCAAGGTACCTTGCGACnTGCCATCTGCGCTCCACCAGTAAATGGACGTCTTCGATCCTTCTGTTGTTGGCGTAGTGCAAACGTTTGGGAAGGTGCTGTTTCAAGTAAGGCTTAAAGTGCTGGTCTGGTTTTTTACACTGAAATATAAATGGACATTGGATTTTGCAATGGAGAGTCTTCTAGAAGAGTCCAAGACATTCTCTCCAGAAAGCTGAAGG | |
| 89 > chr15_64470252_64471048 89 G A | |
| 90 TGTGTGTGTGTGTGTGTGTGTGTGCCTGTGTCTGTACATGCACACCACGTGGCCTCACCCAGTGCCCTCAGCTCCATGGTGATGTCCACnTAGCCGTGCTCCGCGCTGTAGTACATGGCCTCCTGGAGGGCCTTGGTGCGCGTCCGGCTCAGGCGCATGGGCCCCTCGCTGCCGCTGCCCTGGCTGGATGCATCGCTCTCTTCCACGCCCTCAGCCAGGATCTCCTCCAGGGACAGCACATCTGCTTTGGCCTGCTGTGGCTGAGTCAGGAGCTTCCTCAGGACGTTCCT | |
| 91 etc. | |
| 92 </help> | |
| 93 </tool> |