Mercurial > repos > iuc > bedtools
annotate reldist.xml @ 36:0a5c785ac6db draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 833a0b5510d91226c1b0b94550cebfd44243b8d4"
author | iuc |
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date | Mon, 15 Jun 2020 16:55:13 -0400 |
parents | dde39ba9c031 |
children | 3e38c9b3214f |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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1 <tool id="bedtools_reldistbed" name="bedtools ReldistBed" version="@TOOL_VERSION@"> |
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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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2 <description>calculate the distribution of relative distances</description> |
0 | 3 <macros> |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <expand macro="stdio" /> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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8 <command><![CDATA[ |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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9 bedtools reldist |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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10 -a '$inputA' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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11 -b '$inputB' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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12 $detail |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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changeset
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13 > '$output' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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14 ]]></command> |
0 | 15 <inputs> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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diff
changeset
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16 <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/> |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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17 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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18 <param argument="-detail" type="boolean" truevalue="-detail" falsevalue="" checked="false" |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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19 label="Instead of a summary, report the relative distance for each interval in A" /> |
0 | 20 </inputs> |
21 <outputs> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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22 <data name="output" format_source="inputA" metadata_source="inputA" label="Relalative distance of ${inputA.name} and ${inputB.name}"/> |
0 | 23 </outputs> |
1 | 24 <tests> |
25 <test> | |
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
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26 <param name="inputA" value="a.bed" ftype="bed" /> |
a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
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27 <param name="inputB" value="a.bed" ftype="bed" /> |
1 | 28 <output name="output" file="reldistBed_result1.bed" ftype="bed" /> |
29 </test> | |
30 </tests> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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31 <help><![CDATA[ |
0 | 32 **What it does** |
33 | |
1 | 34 Traditional approaches to summarizing the similarity between two sets of genomic intervals are based upon the number or proportion of intersecting intervals. However, such measures are largely blind to spatial correlations between the two sets where, dpesite consistent spacing or proximity, intersections are rare (for example, enhancers and transcription start sites rarely overlap, yet they are much closer to one another than two sets of random intervals). Favorov et al proposed a relative distance metric that describes distribution of relative distances between each interval in one set nd the two closest intervals in another set (see figure above). If there is no spatial correlation between the two sets, one would expect the relative distances to be uniformaly distributed among the relative distances ranging from 0 to 0.5. If, however, the intervals tend to be much closer than expected by chance, the distribution of observed relative distances would be shifted towards low relative distance values (e.g., the figure below). |
0 | 35 |
36 .. image:: $PATH_TO_IMAGES/reldist-glyph.png | |
37 | |
38 .. class:: infomark | |
39 | |
40 @REFERENCES@ | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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41 ]]></help> |
1 | 42 <expand macro="citations"> |
43 <citation type="doi">10.1371/journal.pcbi.1002529</citation> | |
44 </expand> | |
0 | 45 </tool> |