root/galaxy-central/tools/extract/liftOver_wrapper.xml

リビジョン 2, 3.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="liftOver1" name="Convert genome coordinates" version="1.0.2">
2  <description> between assemblies and genomes</description>
3  <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey $minMatch</command>
4  <inputs>
5    <param format="interval" name="input" type="data" label="Convert coordinates of">
6      <validator type="unspecified_build" />
7      <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
8    </param>
9    <param name="to_dbkey" type="select" label="To">
10      <options from_file="liftOver.loc">
11        <column name="name" index="1"/>
12        <column name="value" index="2"/>
13        <column name="dbkey" index="0"/>
14        <filter type="data_meta" ref="input" key="dbkey" column="0" />
15      </options>
16    </param>
17    <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" />
18  </inputs>
19  <outputs>
20    <data format="input" name="out_file1" label="${tool.name} on ${on_string} [ MAPPED COORDINATES ]">
21      <actions>
22        <action type="metadata" name="dbkey">
23          <option type="from_file" name="liftOver.loc" column="1" offset="0">
24            <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
25            <filter type="param_value" ref="to_dbkey" column="2"/>
26          </option>
27        </action>
28      </actions>
29    </data>
30    <data format="input" name="out_file2" label="${tool.name} on ${on_string} [ UNMAPPED COORDINATES ]" />
31  </outputs>
32  <requirements>
33    <requirement type="package">ucsc_tools</requirement>
34  </requirements>
35  <tests>
36    <test>
37      <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
38      <param name="to_dbkey" value="panTro2" />
39      <param name="minMatch" value="0.95" />
40      <output name="out_file1" file="5_liftover_mapped.bed"/>
41      <output name="out_file2" file="5_liftover_unmapped.bed"/>
42    </test>
43  </tests>
44  <help>
45.. class:: warningmark
46
47Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary).
48
49.. class:: warningmark
50
51This tool will only work on interval datasets with chromosome in column 1,
52start co-ordinate in column 2 and end co-ordinate in column 3. BED comments
53and track and browser lines will be ignored, but if other non-interval lines
54are present the tool will return empty output datasets.
55
56-----
57
58.. class:: infomark
59
60**What it does**
61
62This 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.
63
64-----
65
66**Example**
67
68Converting the following hg16 intervals to hg18 intervals::
69
70    chrX  85170   112199  AK002185  0  +
71    chrX  110458  112199  AK097346  0  +
72    chrX  112203  121212  AK074528  0  -
73
74will produce the following hg18 intervals::
75
76    chrX  132991  160020  AK002185  0  +
77    chrX  158279  160020  AK097346  0  +
78    chrX  160024  169033  AK074528  0  -
79
80  </help>
81</tool>
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