/tools/liftover/bedLiftover_wrapper.xml

 1<tool id="liftOver2" name="[Galaxy]Convert genome coordinates" version="1.0.2">
 2  <description> between assemblies and genomes</description>
 3  <command interpreter="python">bedLiftover_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey $minMatch</command>
 4  <inputs>
 5    <param format="interval" name="input" type="data" label="Convert coordinates of">
 6      <validator type="unspecified_build" />
 7      <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
 8    </param>
 9    <param name="to_dbkey" type="select" label="To">
10      <options from_file="liftOver.loc">
11        <column name="name" index="1"/>
12        <column name="value" index="2"/>
13        <column name="dbkey" index="0"/>
14        <filter type="data_meta" ref="input" key="dbkey" column="0" />
15      </options>
16    </param> 
17    <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" />
18  </inputs>
19  <outputs>
20    <data format="input" name="out_file1" />
21    <data format="input" name="out_file2" />
22  </outputs>
23  <requirements>
24    <requirement type="binary">liftOver</requirement>
25  </requirements>
26  <tests>
27    <test>
28      <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
29      <param name="to_dbkey" value="panTro2" />
30      <param name="minMatch" value="0.95" />
31      <output name="out_file1" file="5_liftover_mapped.bed"/>
32      <output name="out_file2" file="5_liftover_unmapped.bed"/>
33    </test>
34  </tests>
35  <help>
36.. class:: warningmark
37
38Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary).
39
40.. class:: warningmark
41
42This tool will only work on interval datasets with chromosome in column 1,
43start co-ordinate in column 2 and end co-ordinate in column 3. BED comments
44and track and browser lines will be ignored, but if other non-interval lines
45are present the tool will return empty output datasets.
46
47-----
48
49.. class:: infomark
50
51**What it does**
52
53This tool converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any. 
54
55-----
56
57**Example**
58
59Converting the following hg16 intervals to hg18 intervals::
60
61    chrX  85170   112199  AK002185  0  +
62    chrX  110458  112199  AK097346  0  +
63    chrX  112203  121212  AK074528  0  -
64
65will produce the following hg18 intervals::
66
67    chrX  132991  160020  AK002185  0  +
68    chrX  158279  160020  AK097346  0  +
69    chrX  160024  169033  AK074528  0  -
70
71  </help>
72  <code file="liftOver_wrapper_code.py" />
73</tool>