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107 lines
3.1 KiB
XML
107 lines
3.1 KiB
XML
<tool id="hgv_add_scores" name="phyloP" version="1.0.0">
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<description>interspecies conservation scores</description>
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<command interpreter="python">
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add_scores.py "$input1" "$out_file1" "${GALAXY_DATA_INDEX_DIR}/add_scores.loc" "${input1.metadata.dbkey}" "${input1.metadata.chromCol}" "${input1.metadata.startCol}"
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</command>
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<inputs>
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<param format="interval" name="input1" type="data" label="Dataset">
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<validator type="unspecified_build"/>
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<validator type="dataset_metadata_in_file" filename="add_scores.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build."/>
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</param>
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</inputs>
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<outputs>
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<data format="input" name="out_file1" />
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</outputs>
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<requirements>
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<requirement type="package">add_scores</requirement>
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</requirements>
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<tests>
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<test>
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<param name="input1" value="add_scores_input1.interval" ftype="interval" dbkey="hg18" />
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<output name="output" file="add_scores_output1.interval" />
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</test>
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<test>
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<param name="input1" value="add_scores_input2.bed" ftype="interval" dbkey="hg18" />
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<output name="output" file="add_scores_output2.interval" />
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</test>
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</tests>
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<help>
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.. class:: warningmark
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This currently works only for builds hg18 and hg19.
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-----
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**Dataset formats**
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The input can be any interval_ format dataset. The output is also in interval format.
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(`Dataset missing?`_)
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.. _interval: ${static_path}/formatHelp.html#interval
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.. _Dataset missing?: ${static_path}/formatHelp.html
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-----
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**What it does**
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This tool adds a column that measures interspecies conservation at each SNP
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position, using conservation scores for primates pre-computed by the
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phyloP program. PhyloP performs an exact P-value computation under a
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continuous Markov substitution model.
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The chromosome and start position
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are used to look up the scores, so if a larger interval is in the input,
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only the score for the first nucleotide is returned.
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-----
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**Example**
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- input file, with SNPs::
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chr22 16440426 14440427 C/T
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chr22 15494851 14494852 A/G
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chr22 14494911 14494912 A/T
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chr22 14550435 14550436 A/G
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chr22 14611956 14611957 G/T
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chr22 14612076 14612077 A/G
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chr22 14668537 14668538 C
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chr22 14668703 14668704 A/T
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chr22 14668775 14668776 G
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chr22 14680074 14680075 A/T
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etc.
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- output file, showing conservation scores for primates::
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chr22 16440426 14440427 C/T 0.509
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chr22 15494851 14494852 A/G 0.427
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chr22 14494911 14494912 A/T NA
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chr22 14550435 14550436 A/G NA
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chr22 14611956 14611957 G/T -2.142
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chr22 14612076 14612077 A/G 0.369
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chr22 14668537 14668538 C 0.419
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chr22 14668703 14668704 A/T -1.462
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chr22 14668775 14668776 G 0.470
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chr22 14680074 14680075 A/T 0.303
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etc.
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"NA" means that the phyloP score was not available.
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-----
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**Reference**
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Siepel A, Pollard KS, Haussler D. (2006)
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New methods for detecting lineage-specific selection.
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In Proceedings of the 10th International Conference on Research in Computational
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Molecular Biology (RECOMB 2006), pp. 190-205.
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</help>
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</tool>
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