/tools/extract/phastOdds/phastOdds_tool.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 67 lines · 53 code · 14 blank · 0 comment · 0 complexity · 296eda54b0eb46e7e978b8a1a1f5a869 MD5 · raw file
- <tool id="phastOdds_for_intervals" name="Compute phastOdds score" version="1.0.0">
- <description>for each interval</description>
- <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>
- <inputs>
- <param format="interval" name="input" type="data" label="Interval file">
- <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."/>
- <validator type="dataset_metadata_in_file" filename="phastOdds.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." />
- </param>
- <param name="score_file" type="select" label="Available datasets">
- <options from_file="phastOdds.loc">
- <column name="name" index="1"/>
- <column name="value" index="2"/>
- <column name="dbkey" index="0"/>
- <filter type="data_meta" ref="input" key="dbkey" column="0" />
- </options>
- </param>
- <param name="per_col" type="boolean" label="Standardize" help="Standardizes the score to be per alignment column" checked="yes" truevalue="-p" falsevalue=""/>
- </inputs>
- <outputs>
- <data format="interval" name="output" metadata_source="input"/>
- </outputs>
- <requirements>
- <requirement type="python-module">numpy</requirement>
- <requirement type="python-module">tables</requirement>
- </requirements>
- <tests>
- <test>
- <param name="input" value="4.bed" dbkey="hg17" ftype="bed"/>
- <param name="score_file" value="/galaxy/data/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds" />
- <param name="per_col" value="true" />
- <output name="output" file="phastOdds_tool_out.interval" />
- </test>
- </tests>
- <help>
-
- .. class:: warningmark
- This tool currently only works with interval data from genome build hg17.
- .. class:: warningmark
- This 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.
- -----
- **Syntax**
- Append a column to each line of an interval file containing the phastOdds score for that interval.
- -----
- **Example**
- If your original data has the following format:
- +-----+-----+---+
- |chrom|start|end|
- +-----+-----+---+
- and you choose to compute phastOdds scores, your output will look like this:
- +-----+-----+---+-----+
- |chrom|start|end|score|
- +-----+-----+---+-----+
- </help>
- </tool>