Mercurial > repos > iuc > resize_coordinate_window
diff resize_coordinate_window.xml @ 1:0164d2edba9f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
author | iuc |
---|---|
date | Tue, 16 Feb 2016 04:05:23 -0500 |
parents | 08b6255afde7 |
children | 9ba78e8985dc |
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--- a/resize_coordinate_window.xml Tue Jan 19 09:34:56 2016 -0500 +++ b/resize_coordinate_window.xml Tue Feb 16 04:05:23 2016 -0500 @@ -1,21 +1,34 @@ -<tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.0"> +<tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.1"> <description>of GFF data</description> <command> python $__tool_directory__/resize_coordinate_window.py --input "$input" + --start_coordinate $start_coordinate --subtract_from_start $subtract_from_start --add_to_end $add_to_end --extend_existing $extend_existing + --chrom_len_file ${chromInfo} + --region_boundaries $region_boundaries --output "$output" </command> <inputs> <param name="input" type="data" format="gff" label="Gff file" /> + <param name="start_coordinate" type="select" label="Start coordinate" help="Input data is 0-based or 1-based"> + <option value="0" selected="True">0</option> + <option value="1">1</option> + </param> <param name="subtract_from_start" type="integer" value="30" min="0" label="Distance to subtract from the start coordinate"/> <param name="add_to_end" type="integer" value="30" min="0" label="Distance to add to the end coordinate"/> <param name="extend_existing" type="select" label="Resize window from" help="The midpoint is computed as (start + end) // 2"> <option value="midpoint" selected="True">the midpoint of the start and end coordinates</option> <option value="existing">the start and end coordinates</option> </param> + <param name="region_boundaries" type="select" label="Handle chromosome boundaries by" help="Expanding the region may result in crossing chromosome start and end coordinate boundaries."> + <option value="discard" selected="True">discarding the region</option> + <option value="limit">keeping the region by limiting the expansion to not cross the start or end coordinate boundary</option> + <option value="nothing">keeping the region by allowing the expansion to cross the start or end coordinate boundary</option> + <option value="error">outputting an error</option> + </param> </inputs> <outputs> <data name="output" format="gff" /> @@ -23,20 +36,43 @@ <tests> <test> <param name="input" value="input.gff" ftype="gff" /> + <param name="start_coordinate" value="1" /> <param name="subtract_from_start" value="13" /> <param name="add_to_end" value="13" /> <param name="extend_existing" value="midpoint" /> + <param name="region_boundaries" value="error" /> <output name="output" file="output.gff" ftype="gff" /> </test> + <test> + <param name="input" value="input.gff" ftype="gff" /> + <param name="start_coordinate" value="0" /> + <param name="subtract_from_start" value="80" /> + <param name="add_to_end" value="80" /> + <param name="extend_existing" value="midpoint" /> + <param name="region_boundaries" value="discard" /> + <output name="output" file="output_discard.gff" ftype="gff" /> + </test> </tests> <help> **What it does** Modifies the start and end coordinates of GFF data such that the new start and end position is based on a -specified window size that is computed either from the existing start and end coordinates or centered on +specified region size that is computed either from the existing start and end coordinates or centered on the midpoint between them. +Region expansion may result in the new start or end coordinates crossing the chromosome boundary. The +chromosome start is set to 0 or 1 using the **Start coordinate** parameter. The end is retrieved from a +file within the Galaxy environment that includes the length of chromosomes for all genome builds. If these +files are missing, the end coordinate is set to 2147483647, which is the maximum value of a signed 32 bit +integer. The **Handle chromosome boundaries by** parameter handles chromosome boundaries that are crossed +by expanding the region using one of the following options. + +* **discarding the region** - the region will be discarded and processing will continue with the next line in the dataset. +* **keeping the region by limiting the expansion to not cross the start or end coordinate boundary** - expansion will be restricted to not cross the chromosome's start or end coordinates for the current region. +* **keeping the region by allowing the expansion to cross the start or end coordinate boundary** - allow defined expansion, crossing the start boundary results in a negative start value. +* **outputting an error** - Stop processing and display an error. + ----- **Example** @@ -47,7 +83,7 @@ chr1 genetrack . 31 51 245 - . stddev=2.66582799529 chr1 genetrack . 40 60 2060 + . stddev=2.7859667372 -Resizing the coordinate window by 13 from the computed midpoint of the start and end coordinates produces:: +Setting start coordinate to 1 and resizing the coordinate window by 13 from the computed midpoint of the start and end coordinates produces:: chr1 genetrack . 14 40 918 + . stddev=5.96715849116 chr1 genetrack . 28 54 245 - . stddev=2.66582799529` @@ -57,7 +93,7 @@ <citations> <citation type="bibtex"> @unpublished{None, - author = {}, + author = {Greg Von Kuster}, title = {None}, year = {None}, eprint = {None},