Mercurial > repos > iuc > bedtools
comparison closestBed.xml @ 5:f8b7dc21b4ee draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
| author | iuc |
|---|---|
| date | Sat, 27 Feb 2016 12:56:56 -0500 |
| parents | 607c0576c6ab |
| children | d25966c8ddeb |
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| 4:607c0576c6ab | 5:f8b7dc21b4ee |
|---|---|
| 41 </param> | 41 </param> |
| 42 | 42 |
| 43 <expand macro="strand2" /> | 43 <expand macro="strand2" /> |
| 44 | 44 |
| 45 <param name="addition" type="boolean" checked="false" truevalue="-d" falsevalue="" | 45 <param name="addition" type="boolean" checked="false" truevalue="-d" falsevalue="" |
| 46 label="In addition to the closest feature in B, report its distance to A as an extra column" | 46 label="In addition to the closest feature in B, report its distance to A as an extra column" |
| 47 help="The reported distance for overlapping features will be 0. (-d)" /> | 47 help="The reported distance for overlapping features will be 0. (-d)" /> |
| 48 | 48 |
| 49 <conditional name="addition2"> | 49 <conditional name="addition2"> |
| 50 <param name="addition2_select" type="select" optional="True" | 50 <param name="addition2_select" type="select" |
| 51 label="Add additional columns to report distance to upstream feature. Distance defintion" | 51 label="Add additional columns to report distance to upstream feature. Distance defintion" |
| 52 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)"> | 52 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)"> |
| 53 <option value="" selected="True">Do not report the distance et all.</option> | 53 <option value="" selected="True">Do not report the distance et all.</option> |
| 54 <option value="ref">Report distance with respect to the reference genome. B features with a lower (start, stop) are upstream. (-ref)</option> | 54 <option value="ref">Report distance with respect to the reference genome. B features with a lower (start, stop) are upstream. (-ref)</option> |
| 55 <option value="a">Report distance with respect to A. When A is on the - strand, "upstream" means B has a higher (start,stop). (-a)</option> | 55 <option value="a">Report distance with respect to A. When A is on the - strand, "upstream" means B has a higher (start,stop). (-a)</option> |
| 56 <option value="b">Report distance with respect to B. When B is on the - strand, "upstream" means A has a higher (start,stop). (-b)</option> | 56 <option value="b">Report distance with respect to B. When B is on the - strand, "upstream" means A has a higher (start,stop). (-b)</option> |
| 69 | 69 |
| 70 <param name="k" type="integer" value="1" optional="True" min="1" | 70 <param name="k" type="integer" value="1" optional="True" min="1" |
| 71 label="Report the k closest hits" help="(-k)"/> | 71 label="Report the k closest hits" help="(-k)"/> |
| 72 | 72 |
| 73 <param name="io" type="boolean" checked="false" truevalue="-io" falsevalue="" | 73 <param name="io" type="boolean" checked="false" truevalue="-io" falsevalue="" |
| 74 label="Ignore features in B that overlap A" | 74 label="Ignore features in B that overlap A" |
| 75 help="That is, we want close, yet not touching features only. (-io)" /> | 75 help="That is, we want close, yet not touching features only. (-io)" /> |
| 76 | 76 |
| 77 <param name="mdb" type="select" optional="True" | 77 <param name="mdb" type="select" optional="True" |
| 78 label="How multiple databases are resolved" | 78 label="How multiple databases are resolved" |
| 79 help="(-mdb)"> | 79 help="(-mdb)"> |
| 80 <option value="each" selected="True">Report closest records for each database. (-each)</option> | 80 <option value="each" selected="True">Report closest records for each database. (-each)</option> |
| 81 <option value="all">Report closest records among all databases. (-all)</option> | 81 <option value="all">Report closest records among all databases. (-all)</option> |
| 82 </param> | 82 </param> |
| 83 </inputs> | 83 </inputs> |
| 84 <outputs> | 84 <outputs> |
| 85 <data format_source="inputA" name="output" metadata_source="inputA" label="Clostest region of ${inputA} in ${inputB}"/> | 85 <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} --> |
| 86 <!-- <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> --> | |
| 87 <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${on_string}"/> | |
| 86 </outputs> | 88 </outputs> |
| 87 <tests> | 89 <tests> |
| 88 <test> | 90 <test> |
| 89 <param name="inputA" value="closestBedA.bed" ftype="bed" /> | 91 <param name="inputA" value="closestBedA.bed" ftype="bed" /> |
| 90 <param name="inputB" value="closestBedB.bed" ftype="bed" /> | 92 <param name="inputB" value="closestBedB.bed" ftype="bed" /> |