Mercurial > repos > iuc > resize_coordinate_window
diff resize_coordinate_window.xml @ 0:08b6255afde7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
author | iuc |
---|---|
date | Tue, 19 Jan 2016 09:34:56 -0500 |
parents | |
children | 0164d2edba9f |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/resize_coordinate_window.xml Tue Jan 19 09:34:56 2016 -0500 @@ -0,0 +1,67 @@ +<tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.0"> + <description>of GFF data</description> + <command> + python $__tool_directory__/resize_coordinate_window.py + --input "$input" + --subtract_from_start $subtract_from_start + --add_to_end $add_to_end + --extend_existing $extend_existing + --output "$output" + </command> + <inputs> + <param name="input" type="data" format="gff" label="Gff file" /> + <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> + </inputs> + <outputs> + <data name="output" format="gff" /> + </outputs> + <tests> + <test> + <param name="input" value="input.gff" ftype="gff" /> + <param name="subtract_from_start" value="13" /> + <param name="add_to_end" value="13" /> + <param name="extend_existing" value="midpoint" /> + <output name="output" file="output.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 +the midpoint between them. + +----- + +**Example** + +If the input dataset is:: + + chr1 genetrack . 17 37 918 + . stddev=5.96715849116 + 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:: + + chr1 genetrack . 14 40 918 + . stddev=5.96715849116 + chr1 genetrack . 28 54 245 - . stddev=2.66582799529` + chr1 genetrack . 37 63 2060 + . stddev=2.7859667372 + + </help> + <citations> + <citation type="bibtex"> + @unpublished{None, + author = {}, + title = {None}, + year = {None}, + eprint = {None}, + url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} + }</citation> + </citations> +</tool>