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/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
 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" "--chrlens_loc=${GALAXY_DATA_INDEX_DIR}/gd.chrlens.loc" "--num_snps=$num_snps"
 6    #if $override_metadata.choice == "0":
 7      "--ref_chrom_col=${input.metadata.ref}" "--ref_pos_col=${input.metadata.rPos}" "--species=${input.metadata.species}"
 8    #else
 9      "--ref_chrom_col=$ref_col" "--ref_pos_col=$rpos_col" "--species=$species"
10    #end if
11  </command>
12
13  <inputs>
14    <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/>
15    <param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/>
16    <conditional name="override_metadata">
17      <param name="choice" type="select" format="integer" label="choose columns">
18        <option value="0" selected="true">No, get columns from metadata</option>
19        <option value="1" >Yes, choose columns</option>
20      </param>
21      <when value="0">
22        <!-- no options -->
23      </when>
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="species" type="select" label="Choose species">
28          <options from_file="gd.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>
38    <data format="wsf" name="output" metadata_source="input"/>
39  </outputs>
40
41  <tests>
42    <test>
43      <param name="input" value="gd.sample.wsf" ftype="wsf"/>
44      <param name="num_snps" value="5"/>
45      <param name="choice" value="0"/>
46      <output name="output" file="gd.select_snps.wsf"/>
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>