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74 lines
2.9 KiB
XML
74 lines
2.9 KiB
XML
<tool id="genetrack1" name="GeneTrack">
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<description>Track creator/viewer</description>
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<code file="genetrack_code.py">
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<hook exec_after_process="exec_after_process" />
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</code>
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<command interpreter="python">
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genetrack.py -l $data_label
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#if not str($fit_data) == "None"
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-1
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${fit_data}:${fit_data.metadata.chromCol}:${fit_data.metadata.positionCol}:${fit_data.metadata.forwardCol}:${fit_data.metadata.reverseCol}
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#end if
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#if $feature_data
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-2
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#end if
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#for $data in $feature_data
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${data.name}:${data.input}:${data.input.metadata.chromCol}:${data.input.metadata.startCol}:${data.input.metadata.endCol}:${data.input.metadata.strandCol}:${data.input.metadata.nameCol},
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#end for
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-d ${genetrack.files_path}
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-o ${bed_out}
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</command>
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<inputs>
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<param name="data_label" type="text" label="Track Label" size="50">
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<validator type="regex" message="Please name the track with only alphanumeric characters.">[a-zA-Z0-9]{1,25}</validator>
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</param>
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<param name="fit_data" type="data" format="coverage" label="Coverage Dataset (optional)" optional="true" />
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<repeat name="feature_data" title="Features">
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<param name="input" type="data" format="interval" label="Dataset" />
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<param name="name" type="text" label="Feature Type (mRNA, ESTs, ORFs, etc.)" size="25">
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<validator type="regex" message="Please name the feature with only alphanumeric characters.">[a-zA-Z0-9]{1,25}</validator>
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</param>
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</repeat>
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</inputs>
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<outputs>
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<data format="genetrack" name="genetrack" />
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<data format="bed" name="bed_out" />
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</outputs>
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<requirements>
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<requirement type="python-module">tables</requirement>
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<requirement type="python-module">atlas</requirement>
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<requirement type="python-module">pychartdir</requirement>
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<requirement type="python-module">numpy</requirement>
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</requirements>
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<help>
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This tool takes the input Fit Data and creates a peak and curve plot
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showing the reads and fitness on each basepair. Features can be
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plotted below as tracks. Fit data is coverage output from tools like
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the Lastz tool. Features are simply interval datasets that may be
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plotted as tracks below the optional fit data. Both the fit data and
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feature datasets are optional, but at least one of either is required
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to generate a track.
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-----
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**Syntax**
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- **Track Label** is the name of the generated track.
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- **Fit Data** is the dataset to calculate coverage/reads across
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basepairs and generate a curve. This is optional, and tracks may
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be created simply showing features.
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- **Features** are datasets (interval format) to be plotted as tracks.
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These are also optional, but at least 1 feature track or 1 fit
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data is required to generate a track.
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</help>
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</tool>
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