Mercurial > repos > xuebing > sharplabtool
comparison 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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| -1:000000000000 | 0:9071e359b9a3 |
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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 | |
| 38 This tool currently only works with interval data from genome build hg17. | |
| 39 | |
| 40 .. class:: warningmark | |
| 41 | |
| 42 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. | |
| 43 | |
| 44 ----- | |
| 45 | |
| 46 **Syntax** | |
| 47 | |
| 48 Append a column to each line of an interval file containing the phastOdds score for that interval. | |
| 49 | |
| 50 ----- | |
| 51 | |
| 52 **Example** | |
| 53 | |
| 54 If your original data has the following format: | |
| 55 | |
| 56 +-----+-----+---+ | |
| 57 |chrom|start|end| | |
| 58 +-----+-----+---+ | |
| 59 | |
| 60 and 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> |