Previous changeset 4:607c0576c6ab (2016-01-27) Next changeset 6:d25966c8ddeb (2016-05-22) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c |
modified:
closestBed.xml |
b |
diff -r 607c0576c6ab -r f8b7dc21b4ee closestBed.xml --- a/closestBed.xml Wed Jan 27 15:15:59 2016 -0500 +++ b/closestBed.xml Sat Feb 27 12:56:56 2016 -0500 |
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@@ -43,12 +43,12 @@ <expand macro="strand2" /> <param name="addition" type="boolean" checked="false" truevalue="-d" falsevalue="" - label="In addition to the closest feature in B, report its distance to A as an extra column" + label="In addition to the closest feature in B, report its distance to A as an extra column" help="The reported distance for overlapping features will be 0. (-d)" /> <conditional name="addition2"> - <param name="addition2_select" type="select" optional="True" - label="Add additional columns to report distance to upstream feature. Distance defintion" + <param name="addition2_select" type="select" + label="Add additional columns to report distance to upstream feature. Distance defintion" help="Like -d, report the closest feature in B, and its distance to A as an extra column. However unlike -d, use negative distances to report upstream features. (-D)"> <option value="" selected="True">Do not report the distance et all.</option> <option value="ref">Report distance with respect to the reference genome. B features with a lower (start, stop) are upstream. (-ref)</option> @@ -71,18 +71,20 @@ label="Report the k closest hits" help="(-k)"/> <param name="io" type="boolean" checked="false" truevalue="-io" falsevalue="" - label="Ignore features in B that overlap A" + label="Ignore features in B that overlap A" help="That is, we want close, yet not touching features only. (-io)" /> <param name="mdb" type="select" optional="True" - label="How multiple databases are resolved" + label="How multiple databases are resolved" help="(-mdb)"> <option value="each" selected="True">Report closest records for each database. (-each)</option> <option value="all">Report closest records among all databases. (-all)</option> </param> </inputs> <outputs> - <data format_source="inputA" name="output" metadata_source="inputA" label="Clostest region of ${inputA} in ${inputB}"/> + <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} --> + <!-- <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> --> + <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${on_string}"/> </outputs> <tests> <test> |