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annotate select_snps.xml @ 32:03c22b722882

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remove BeautifulSoup dependency
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:54:23 -0400
parents d6b961721037
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1 <tool id="gd_select_snps" name="Sample SNPs" version="1.0.0">
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2 <description>: Select a specified number of SNPs, uniformly spaced</description>
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3
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4 <command interpreter="python">
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5 select_snps.py "--input=$input" "--output=$output" "--index_dir=$GALAXY_DATA_INDEX_DIR" "--num_snps=$num_snps"
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6 #if $override_metadata.choice == "0":
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7 "--ref_chrom_col=${input.metadata.ref}" "--ref_pos_col=${input.metadata.rPos}" "--ref_species=${input.metadata.dbkey}"
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8 #else
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9 "--ref_chrom_col=$ref_col" "--ref_pos_col=$rpos_col" "--ref_species=$ref_species"
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10 #end if
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11 </command>
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13 <inputs>
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14 <param format="tabular" name="input" type="data" label="SNP dataset">
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15 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
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16 </param>
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17 <param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/>
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18 <conditional name="override_metadata">
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19 <param name="choice" type="select" format="integer" label="Choose columns" help="Datasets in gd_snp format have the column information in the metadata, all others must be chosen." >
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20 <option value="0" selected="true">No, get columns from metadata</option>
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21 <option value="1" >Yes, choose columns</option>
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22 </param>
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23 <when value="0" />
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24 <when value="1">
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25 <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome"/>
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26 <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position"/>
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27 <param name="ref_species" type="select" label="Choose reference species">
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28 <options from_file="gd.ref_species.txt">
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29 <column name="name" index="1"/>
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30 <column name="value" index="0"/>
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31 </options>
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32 </param>
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33 </when>
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34 </conditional>
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35 </inputs>
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36
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37 <outputs>
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38 <data format="gd_snp" name="output" metadata_source="input"/>
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39 </outputs>
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40
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41 <tests>
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42 <test>
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43 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp"/>
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44 <param name="num_snps" value="100"/>
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45 <param name="choice" value="0"/>
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46 <output name="output" file="test_out/select_snps/select_snps.gd_snp" />
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47 </test>
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48 </tests>
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50
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51 <help>
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52
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53 **Dataset formats**
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54
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55 The input and output datasets are in tabular_ format.
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56 (`Dataset missing?`_)
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57
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58 .. _tabular: ./static/formatHelp.html#tab
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59 .. _Dataset missing?: ./static/formatHelp.html
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60
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61 -----
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62
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63 **What it does**
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64
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65 This tool attempts to select a specified number of SNPs from the dataset, making
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66 them approximately uniformly spaced relative to the reference genome. The number
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67 actually selected may be slightly more than the specified number.
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68
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69 -----
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70
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71 **Example**
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73 - input (gd_snp format)::
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74
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75 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
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76 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
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77 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
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78 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
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79 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
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80 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
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81 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
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82 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
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83 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
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84 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
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85 etc.
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86
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87 - output::
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89 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
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90 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
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91 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
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92 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
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93 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
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94 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
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95 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
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96 etc.
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97
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98 </help>
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99 </tool>