/tools/genome_diversity/select_snps.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 87 lines · 73 code · 13 blank · 1 comment · 0 complexity · 95ff6ec39bde036fbc6e967216a5a4ee MD5 · raw file
- <tool id="gd_select_snps" name="Select" version="1.0.0">
- <description>a specified number of SNPs</description>
- <command interpreter="python">
- select_snps.py "--input=$input" "--output=$output" "--chrlens_loc=${GALAXY_DATA_INDEX_DIR}/gd.chrlens.loc" "--num_snps=$num_snps"
- #if $override_metadata.choice == "0":
- "--ref_chrom_col=${input.metadata.ref}" "--ref_pos_col=${input.metadata.rPos}" "--species=${input.metadata.species}"
- #else
- "--ref_chrom_col=$ref_col" "--ref_pos_col=$rpos_col" "--species=$species"
- #end if
- </command>
- <inputs>
- <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/>
- <param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/>
- <conditional name="override_metadata">
- <param name="choice" type="select" format="integer" label="choose columns">
- <option value="0" selected="true">No, get columns from metadata</option>
- <option value="1" >Yes, choose columns</option>
- </param>
- <when value="0">
- <!-- no options -->
- </when>
- <when value="1">
- <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome"/>
- <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position"/>
- <param name="species" type="select" label="Choose species">
- <options from_file="gd.species.txt">
- <column name="name" index="1"/>
- <column name="value" index="0"/>
- </options>
- </param>
- </when>
- </conditional>
- </inputs>
- <outputs>
- <data format="wsf" name="output" metadata_source="input"/>
- </outputs>
- <tests>
- <test>
- <param name="input" value="gd.sample.wsf" ftype="wsf"/>
- <param name="num_snps" value="5"/>
- <param name="choice" value="0"/>
- <output name="output" file="gd.select_snps.wsf"/>
- </test>
- </tests>
- <help>
- **What it does**
- It attempts to select a specified number of SNPs from the dataset, making them
- approximately uniformly spaced relative to the reference genome. The number
- actually selected may be slightly more than the specified number.
- -----
- **Example**
- - input file::
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- etc.
- - output file::
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- etc.
- </help>
- </tool>