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1 <tool id="phastOdds_for_intervals" name="Compute phastOdds score" version="1.0.0">
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2 <description>for each interval</description>
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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>
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4 <inputs>
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5 <param format="interval" name="input" type="data" label="Interval file">
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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."/>
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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." />
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8 </param>
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9 <param name="score_file" type="select" label="Available datasets">
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10 <options from_file="phastOdds.loc">
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11 <column name="name" index="1"/>
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12 <column name="value" index="2"/>
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13 <column name="dbkey" index="0"/>
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14 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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15 </options>
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16 </param>
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17 <param name="per_col" type="boolean" label="Standardize" help="Standardizes the score to be per alignment column" checked="yes" truevalue="-p" falsevalue=""/>
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18 </inputs>
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19 <outputs>
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20 <data format="interval" name="output" metadata_source="input"/>
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21 </outputs>
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22 <requirements>
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23 <requirement type="python-module">numpy</requirement>
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24 <requirement type="python-module">tables</requirement>
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25 </requirements>
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26 <tests>
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27 <test>
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28 <param name="input" value="4.bed" dbkey="hg17" ftype="bed"/>
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29 <param name="score_file" value="/galaxy/data/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds" />
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30 <param name="per_col" value="true" />
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31 <output name="output" file="phastOdds_tool_out.interval" />
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32 </test>
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33 </tests>
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34 <help>
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35
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36 .. class:: warningmark
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37
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38 This tool currently only works with interval data from genome build hg17.
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39
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40 .. class:: warningmark
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41
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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.
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43
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44 -----
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45
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46 **Syntax**
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47
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48 Append a column to each line of an interval file containing the phastOdds score for that interval.
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49
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50 -----
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51
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52 **Example**
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53
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54 If your original data has the following format:
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55
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56 +-----+-----+---+
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57 |chrom|start|end|
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58 +-----+-----+---+
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59
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60 and you choose to compute phastOdds scores, your output will look like this:
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61
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62 +-----+-----+---+-----+
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63 |chrom|start|end|score|
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64 +-----+-----+---+-----+
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65
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66 </help>
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67 </tool>
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