Mercurial > repos > xuebing > sharplabtool
diff tools/extract/phastOdds/phastOdds_tool.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/extract/phastOdds/phastOdds_tool.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,67 @@ +<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>