mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
63 lines
2.4 KiB
XML
63 lines
2.4 KiB
XML
<tool id="genetrack1" name="GeneTrack">
|
|
|
|
<description>Track creator/viewer</description>
|
|
|
|
<code file="genetrack_code.py">
|
|
<hook exec_after_process="exec_after_process" />
|
|
</code>
|
|
|
|
<command interpreter="python">
|
|
genetrack.py -l $data_label
|
|
#if not str($fit_data) == "None"
|
|
-1
|
|
${fit_data}:${fit_data.metadata.chromCol}:${fit_data.metadata.positionCol}:${fit_data.metadata.forwardCol}:${fit_data.metadata.reverseCol}
|
|
#end if
|
|
#if $feature_data
|
|
-2
|
|
#end if
|
|
#for $data in $feature_data
|
|
${data.name}:${data.input}:${data.input.metadata.chromCol}:${data.input.metadata.startCol}:${data.input.metadata.endCol}:${data.input.metadata.strandCol}:${data.input.metadata.nameCol},
|
|
#end for
|
|
-d ${genetrack.files_path}
|
|
-o ${bed_out}
|
|
</command>
|
|
|
|
<inputs>
|
|
<param name="data_label" type="text" label="Track Label" size="50">
|
|
<validator type="regex" message="Please name the track with only alphanumeric characters.">[a-zA-Z0-9]{0,25}</validator>
|
|
</param>
|
|
<param name="fit_data" type="data" format="coverage" label="Coverage Dataset" optional="true" />
|
|
<repeat name="feature_data" title="Features">
|
|
<param name="input" type="data" format="interval" label="Dataset" />
|
|
<param name="name" type="text" label="Feature Type (mRNA, ESTs, ORFs, etc.)" size="25">
|
|
<validator type="regex" message="Please name the feature with only alphanumeric characters.">[a-zA-Z0-9]{0,25}</validator>
|
|
</param>
|
|
</repeat>
|
|
</inputs>
|
|
|
|
<outputs>
|
|
<data format="genetrack" name="genetrack" />
|
|
<data format="bed" name="bed_out" />
|
|
</outputs>
|
|
|
|
<requirements>
|
|
<requirement type="python-module">tables</requirement>
|
|
<requirement type="python-module">atlas</requirement>
|
|
<requirement type="python-module">pychartdir</requirement>
|
|
<requirement type="python-module">numpy</requirement>
|
|
</requirements>
|
|
<help>
|
|
This tool takes the input Fit Data and creates a peak and curve plot showing
|
|
the reads and fitness on each basepair. Features can be plotted below as tracks.
|
|
|
|
-----
|
|
|
|
**Syntax**
|
|
|
|
- **Track Label** is the name of the generated track.
|
|
- **Fit Data** are the datasets to calculate coverage/reads across basepairs and generate a curve.
|
|
- **Features** are additional datasets (interval format) to be plotted below as tracks.
|
|
|
|
</help>
|
|
</tool>
|