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/tools/extract/phastOdds/phastOdds_tool.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="phastOdds_for_intervals" name="Compute phastOdds score" version="1.0.0">
 2  <description>for each interval</description>
 3  <command interpreter="python">get_scores_galaxy.py $per_col ${score_file}.h5 ${score_file}.mapping.bed $input $output ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol}</command>
 4  <inputs>
 5    <param format="interval" name="input" type="data" label="Interval file">
 6      <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg17. Click the pencil icon in your history item to set the genome build."/>
 7      <validator type="dataset_metadata_in_file" filename="phastOdds.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." />
 8    </param>
 9    <param name="score_file" type="select" label="Available datasets">
10      <options from_file="phastOdds.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="per_col" type="boolean" label="Standardize" help="Standardizes the score to be per alignment column" checked="yes" truevalue="-p" falsevalue=""/>
18  </inputs>
19  <outputs>
20    <data format="interval" name="output" metadata_source="input"/>
21  </outputs>
22  <requirements>
23    <requirement type="python-module">numpy</requirement>
24    <requirement type="python-module">tables</requirement>
25  </requirements>
26  <tests>
27    <test>
28      <param name="input" value="4.bed" dbkey="hg17" ftype="bed"/>
29      <param name="score_file" value="/galaxy/data/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds" />
30      <param name="per_col" value="true" />
31      <output name="output" file="phastOdds_tool_out.interval" />
32    </test>
33  </tests>
34  <help>
35    
36.. class:: warningmark
37
38This tool currently only works with interval data from genome build hg17.
39
40.. class:: warningmark
41
42This tool assumes that the input dataset is in interval format and contains at least a chrom column, a start column and an end column.  These 3 columns can be dispersed throughout any number of other data columns. 
43
44-----
45
46**Syntax**
47
48Append a column to each line of an interval file containing the phastOdds score for that interval.
49
50-----
51
52**Example**
53
54If your original data has the following format:
55
56+-----+-----+---+
57|chrom|start|end|
58+-----+-----+---+
59
60and you choose to compute phastOdds scores, your output will look like this:
61
62+-----+-----+---+-----+
63|chrom|start|end|score|
64+-----+-----+---+-----+
65
66  </help>
67</tool>