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First pass at final phase of cleaning up approach to dynamic select lists. Added a functional test to phastOdds tool. The following tools now use this latest approach to dynamic optioons:

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axt_to_fasta, phastOdds, axt_to_lav, random_intervals, extractAxt_wrapper, axt_to_concat_fasta, aggregate_binned_scores.
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Greg Von Kuster
2007-11-16 20:08:31 +00:00
parent e97522b3a5
commit 71d16671bc
12 changed files with 365 additions and 221 deletions
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tools/encode/random_intervals.xml
+39 -31
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<tool id="random_intervals1" name="Random Intervals">
<description>create a random set of intervals</description>
<command interpreter="python2.4">random_intervals_no_bits.py $regions $input2 $input1 $out_file1 $input2_chromCol $input2_startCol $input2_endCol $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol $use_mask $strand_overlaps</command>
<inputs>
<page>
<param name="input1" type="data" format="interval" label="File to Mimick"/>
<param name="input2" type="data" format="interval" label="Intervals to Mask"/>
<param name="use_mask" type="select">
<label>Use Mask</label>
<option value="no_mask">No</option>
<option value="use_mask">Yes</option>
</param>
<param name="strand_overlaps" type="select">
<label>Allow overlaps</label>
<option value="all">Any</option>
<option value="strand">Across Strands</option>
<option value="none">None</option>
</param>
</page>
<page>
<param name="regions" label="Regions to use" type="select" dynamic_options="get_available_data( input1.dbkey )"/>
</page>
</inputs>
<outputs>
<data name="out_file1" format="bed"/>
</outputs>
<help>
This tool will attempt to create a random set of intervals that mimic those found within your source file. You may also specify a set of intervals to mask.
<inputs>
<param name="input1" type="data" format="interval" label="File to Mimick"/>
<param name="input2" type="data" format="interval" label="Intervals to Mask"/>
<param name="use_mask" type="select" label="Use mask">
<option value="no_mask">No</option>
<option value="use_mask">Yes</option>
</param>
<param name="strand_overlaps" type="select" label="Allow overlaps">
<option value="all">Any</option>
<option value="strand">Across Strands</option>
<option value="none">None</option>
</param>
<param name="regions" type="select" label="Regions to use">
<options from_file="/depot/data2/galaxy/regions.loc" name_col="1" value_col="2" >
<filter type="data_meta" data_ref="input1" key="build" value="dbkey" col="0" />
</options>
</param>
</inputs>
<outputs>
<data name="out_file1" format="input"/>
</outputs>
<help>
There are several overlap options:
* Across Strands: Random regions are allowed to overlap only if they are on different strands.
* Any: All overlaps are allowed.
* None: No overlapping regions are allowed.
.. class:: warningmark
The second step will let you select a bounding region of interest.
This tool currently only works with data from genome builds hg16 or hg17.
-----
.. class:: infomark
**Note:** If you do not wish to mask a set of intervals, change the Use Mask option to No, this option will override any Mask files selected.
-----
**Syntax**
This tool will attempt to create a random set of intervals that mimic those found within your source file. You may also specify a set of intervals to mask.
**Allow overlaps** options
* **Across Strands** Random regions are allowed to overlap only if they are on different strands.
* **Any** All overlaps are allowed.
* **None** No overlapping regions are allowed.
**Regions to use** options
* Bounding region of interest based on the dataset build.
</help>
<code file="random_intervals_code.py"/>
</tool>