Mercurial > repos > miller-lab > genome_diversity
annotate select_snps.xml @ 7:e29f4d801bb0
change wsf -> snp; wpf -> sap
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Wed, 18 Apr 2012 11:12:21 -0400 |
| parents | 2c498d40ecde |
| children | 9b92372de9f6 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gd_select_snps" name="Select" version="1.0.0"> |
| 2 <description>a specified number of SNPs</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 select_snps.py "--input=$input" "--output=$output" "--index_dir=$GALAXY_DATA_INDEX_DIR" "--num_snps=$num_snps" | |
| 6 #if $override_metadata.choice == "0": | |
| 7 "--ref_chrom_col=${input.metadata.ref}" "--ref_pos_col=${input.metadata.rPos}" "--ref_species=${input.metadata.dbkey}" | |
| 8 #else | |
| 9 "--ref_chrom_col=$ref_col" "--ref_pos_col=$rpos_col" "--ref_species=$ref_species" | |
| 10 #end if | |
| 11 </command> | |
| 12 | |
| 13 <inputs> | |
| 14 <param format="tabular" name="input" type="data" label="Selected SNPS dataset"> | |
| 15 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> | |
| 16 </param> | |
| 17 <param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/> | |
| 18 <conditional name="override_metadata"> | |
| 19 <param name="choice" type="select" format="integer" label="choose columns"> | |
| 20 <option value="0" selected="true">No, get columns from metadata</option> | |
| 21 <option value="1" >Yes, choose columns</option> | |
| 22 </param> | |
| 23 <when value="0" /> | |
| 24 <when value="1"> | |
| 25 <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome"/> | |
| 26 <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position"/> | |
| 27 <param name="ref_species" type="select" label="Choose reference species"> | |
| 28 <options from_file="gd.ref_species.txt"> | |
| 29 <column name="name" index="1"/> | |
| 30 <column name="value" index="0"/> | |
| 31 </options> | |
| 32 </param> | |
| 33 </when> | |
| 34 </conditional> | |
| 35 </inputs> | |
| 36 | |
| 37 <outputs> | |
|
7
e29f4d801bb0
change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
38 <data format="snp" name="output" metadata_source="input"/> |
| 0 | 39 </outputs> |
| 40 | |
| 41 <tests> | |
| 42 <test> | |
|
7
e29f4d801bb0
change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
43 <param name="input" value="test_in/sample.snp" ftype="snp"/> |
| 0 | 44 <param name="num_snps" value="100"/> |
| 45 <param name="choice" value="0"/> | |
|
7
e29f4d801bb0
change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
46 <output name="output" file="test_out/select_snps/select_snps.snp" /> |
| 0 | 47 </test> |
| 48 </tests> | |
| 49 | |
| 50 | |
| 51 <help> | |
| 52 **What it does** | |
| 53 | |
| 54 It attempts to select a specified number of SNPs from the dataset, making them | |
| 55 approximately uniformly spaced relative to the reference genome. The number | |
| 56 actually selected may be slightly more than the specified number. | |
| 57 | |
| 58 ----- | |
| 59 | |
| 60 **Example** | |
| 61 | |
| 62 - input file:: | |
| 63 | |
| 64 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 | |
| 65 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 | |
| 66 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 | |
| 67 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 | |
| 68 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 | |
| 69 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 | |
| 70 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 | |
| 71 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 | |
| 72 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 | |
| 73 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 | |
| 74 etc. | |
| 75 | |
| 76 - output file:: | |
| 77 | |
| 78 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 | |
| 79 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 | |
| 80 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 | |
| 81 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 | |
| 82 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 | |
| 83 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 | |
| 84 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 | |
| 85 etc. | |
| 86 </help> | |
| 87 </tool> |