Mercurial > repos > iuc > bedtools
annotate closestBed.xml @ 30:db1841942d2b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b67e138b17f7e8cb34f59bed0925f691ec9740f3
author | iuc |
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date | Fri, 17 Aug 2018 05:42:39 -0400 |
parents | 95a3b2c25bd1 |
children | 4f7a5ccd2ae9 |
rev | line source |
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0 | 1 <tool id="bedtools_closestbed" name="ClosestBed" version="@WRAPPER_VERSION@.0"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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2 <description>find the closest, potentially non-overlapping interval</description> |
0 | 3 <macros> |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <expand macro="stdio" /> | |
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b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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8 <command><![CDATA[ |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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9 closestBed |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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10 $strand |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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11 $addition |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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12 #if $addition2.addition2_select: |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
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13 -D $addition2.addition2_select |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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14 $addition2.iu |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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15 $addition2.id |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
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16 #end if |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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17 $io |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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18 -mdb $mdb |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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19 -t $ties |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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20 #if str($k): |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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21 -k $k |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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22 #end if |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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23 -a '$inputA' |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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24 #if str($overlap_with.source) == "data_table": |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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25 -b '$overlap_with.table.fields.path' |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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26 #else |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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27 #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.inputB]) |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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28 -b '$inputBs' |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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29 #end if |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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30 > '$output' |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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31 ]]></command> |
0 | 32 <inputs> |
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95a3b2c25bd1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
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33 <param name="inputA" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
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b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
parents:
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changeset
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34 <!-- overlap with file (inputB) --> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
parents:
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changeset
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35 <conditional name="overlap_with"> |
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95a3b2c25bd1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
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36 <param name="source" type="select" label="Overlap with: will you select a @STD_BEDTOOLS_INPUT_LABEL@ file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome"> |
95a3b2c25bd1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
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37 <option value="history" selected="true">Use a @STD_BEDTOOLS_INPUT_LABEL@ file from the history</option> |
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b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
parents:
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38 <option value="data_table">Use a built-in GFF file</option> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
parents:
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changeset
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39 </param> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
parents:
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changeset
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40 <when value="data_table"> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
parents:
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changeset
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41 <param name="table" type="select" label="Select reference GFF" help="If your genome of interest is not listed, contact the Galaxy team"> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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42 <options from_data_table="all_gff"> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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43 <filter type="sort_by" column="2"/> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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44 <validator type="no_options" message="No files are available"/> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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45 </options> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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46 </param> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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47 </when> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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48 <when value="history"> |
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95a3b2c25bd1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
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49 <param name="inputB" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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50 </when> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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51 </conditional> |
0 | 52 |
1 | 53 <param name="ties" type="select" |
54 label="How ties for closest feature should be handled" | |
55 help="This occurs when two features in B have exactly the same overlap with a feature in A."> | |
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b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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56 <option value="all" selected="true">all - Report all ties (default)</option> |
0 | 57 <option value="first">first - Report the first tie that occurred in the B file</option> |
58 <option value="last">last - Report the last tie that occurred in the B file</option> | |
59 </param> | |
60 | |
1 | 61 <expand macro="strand2" /> |
62 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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63 <param name="addition" argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
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64 label="In addition to the closest feature in B, report its distance to A as an extra column" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
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65 help="The reported distance for overlapping features will be 0" /> |
1 | 66 |
67 <conditional name="addition2"> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
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68 <param name="addition2_select" argument="-D" type="select" |
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f8b7dc21b4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
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69 label="Add additional columns to report distance to upstream feature. Distance defintion" |
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b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
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70 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"> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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71 <option value="" selected="true">Do not report the distance et all.</option> |
1 | 72 <option value="ref">Report distance with respect to the reference genome. B features with a lower (start, stop) are upstream. (-ref)</option> |
73 <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> | |
74 <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> | |
75 </param> | |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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76 <when value="" /> |
1 | 77 <when value="ref"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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78 <expand macro="closest_D_option" /> |
1 | 79 </when> |
80 <when value="a"> | |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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81 <expand macro="closest_D_option" /> |
1 | 82 </when> |
83 <when value="b"> | |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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84 <expand macro="closest_D_option" /> |
1 | 85 </when> |
86 </conditional> | |
87 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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88 <param argument="-k" type="integer" min="1" value="1" optional="true" |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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89 label="Report the k closest hits" /> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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90 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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91 <param argument="-io" type="boolean" truevalue="-io" falsevalue="" checked="false" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
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92 label="Ignore features in B that overlap A" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
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93 help="That is, we want close, yet not touching features only" /> |
1 | 94 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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95 <param argument="-mdb" type="select" |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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96 label="How multiple databases are resolved"> |
b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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97 <option value="each" selected="true">Report closest records for each database. (-each)</option> |
1 | 98 <option value="all">Report closest records among all databases. (-all)</option> |
99 </param> | |
0 | 100 </inputs> |
101 <outputs> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
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102 <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} --> |
f8b7dc21b4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
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103 <!-- <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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104 <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" /> |
0 | 105 </outputs> |
1 | 106 <tests> |
107 <test> | |
108 <param name="inputA" value="closestBedA.bed" ftype="bed" /> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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109 <param name="source" value="history" /> |
1 | 110 <param name="inputB" value="closestBedB.bed" ftype="bed" /> |
111 <output name="output" file="closestBed_result1.bed" ftype="bed" /> | |
112 </test> | |
113 <test> | |
114 <param name="inputA" value="closestBed_a.bed" ftype="bed" /> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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115 <param name="source" value="history" /> |
1 | 116 <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> |
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b73962f8fcbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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117 <param name="addition" value="true" /> |
1 | 118 <output name="output" file="closestBed_result2.bed" ftype="bed" /> |
119 </test> | |
120 <test> | |
121 <param name="inputA" value="closestBed_a.bed" ftype="bed" /> | |
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122 <param name="source" value="history" /> |
1 | 123 <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> |
124 <param name="addition" value="True" /> | |
125 <param name="mdb" value="all" /> | |
126 <output name="output" file="closestBed_result3.bed" ftype="bed" /> | |
127 </test> | |
128 <test> | |
129 <param name="inputA" value="closestBed_c.bed" ftype="bed" /> | |
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130 <param name="source" value="history" /> |
1 | 131 <param name="inputB" value="closestBed_d.bed" ftype="bed" /> |
132 <param name="addition2_select" value="ref" /> | |
133 <output name="output" file="closestBed_result4.bed" ftype="bed" /> | |
134 </test> | |
135 <test> | |
136 <param name="inputA" value="closestBed_c.bed" ftype="bed" /> | |
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137 <param name="source" value="history" /> |
1 | 138 <param name="inputB" value="closestBed_d.bed" ftype="bed" /> |
139 <param name="addition2_select" value="a" /> | |
140 <output name="output" file="closestBed_result5.bed" ftype="bed" /> | |
141 </test> | |
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142 <test> |
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143 <param name="inputA" value="closestBedA.bed" ftype="bed" /> |
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144 <param name="source" value="history" /> |
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145 <param name="inputB" value="a.bed" ftype="bed" /> |
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146 <param name="k" value="3" /> |
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147 <output name="output" file="closestBed_result6.bed" ftype="bed" /> |
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148 </test> |
1 | 149 </tests> |
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150 <help><![CDATA[ |
0 | 151 **What it does** |
152 | |
153 Similar to intersectBed, closestBed searches for overlapping features in A and B. In the event that no feature in B overlaps the current feature in A, closestBed will report the closest (that is, least genomic distance from the start or end of A) feature in B. For example, one might want to find which is the closest gene to a significant GWAS polymorphism. Note that closestBed will report an overlapping feature as the closest—that is, it does not restrict to closest non-overlapping feature. | |
154 | |
1 | 155 .. image:: $PATH_TO_IMAGES/closest-glyph.png |
156 | |
0 | 157 @REFERENCES@ |
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158 ]]></help> |
0 | 159 <expand macro="citations" /> |
160 </tool> |