Mercurial > repos > iuc > bedtools
annotate sortBed.xml @ 43:07e8b80f278c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author | iuc |
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date | Fri, 01 Apr 2022 19:02:51 +0000 |
parents | 7ab85ac5f64b |
children | 589e7e57fd6d |
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43
07e8b80f278c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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1 <tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
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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>order the intervals</description> |
0 | 3 <macros> |
4 <import>macros.xml</import> | |
5 </macros> | |
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7ab85ac5f64b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
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6 <expand macro="bio_tools" /> |
0 | 7 <expand macro="requirements" /> |
8 <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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9 <command><![CDATA[ |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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10 sortBed |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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11 -i '$input' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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12 $option |
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07e8b80f278c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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13 @GENOME_FILE@ |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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14 > '$output' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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15 ]]></command> |
0 | 16 <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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17 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" /> |
0 | 18 <param name="option" type="select" label="Sort by"> |
19 <!-- sort -k 1,1 -k2,2 -n a.bed --> | |
20 <option value="">chromosome, then by start position (asc)</option> | |
21 <option value="-sizeA">feature size in ascending order.</option> | |
22 <option value="-sizeD">feature size in descending order.</option> | |
23 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option> | |
24 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option> | |
25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option> | |
26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option> | |
27 </param> | |
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07e8b80f278c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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28 <expand macro="input_conditional_genome_file" help="Sort according to the chromosomes declared in a genome file" /> |
0 | 29 </inputs> |
30 <outputs> | |
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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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31 <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/> |
0 | 32 </outputs> |
1 | 33 <tests> |
34 <test> | |
35 <param name="input" value="sortBed1.bed" ftype="bed" /> | |
36 <param name="option" value="" /> | |
37 <output name="output" file="sortBed_result1.bed" ftype="bed" /> | |
38 </test> | |
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ce3c7f062223
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
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39 <test> |
ce3c7f062223
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents:
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40 <param name="input" value="sortBed2.bed" ftype="bed" /> |
ce3c7f062223
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents:
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changeset
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41 <param name="option" value="" /> |
ce3c7f062223
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents:
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changeset
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42 <output name="output" file="sortBed_result2.bed" ftype="bed" /> |
ce3c7f062223
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents:
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43 </test> |
ce3c7f062223
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents:
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changeset
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44 <test> |
ce3c7f062223
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents:
34
diff
changeset
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45 <param name="input" value="sortBed2.bed" ftype="bed" /> |
ce3c7f062223
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents:
34
diff
changeset
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46 <param name="option" value="" /> |
43
07e8b80f278c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
41
diff
changeset
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47 <conditional name="genome_file_opts"> |
07e8b80f278c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
41
diff
changeset
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48 <param name="genome_file_opts_selector" value="hist" /> |
07e8b80f278c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
41
diff
changeset
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49 <param name="genome" value="mm9.len" ftype="bed" /> |
07e8b80f278c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
41
diff
changeset
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50 </conditional> |
37
ce3c7f062223
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents:
34
diff
changeset
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51 <output name="output" file="sortBed_result3.bed" ftype="bed" /> |
ce3c7f062223
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents:
34
diff
changeset
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52 </test> |
1 | 53 </tests> |
34
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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54 <help><![CDATA[ |
0 | 55 **What it does** |
56 | |
57 Sorts a feature file by chromosome and other criteria. | |
58 | |
59 | |
60 .. class:: warningmark | |
61 | |
62 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility | |
63 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file | |
64 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed | |
65 | |
66 @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
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67 ]]></help> |
0 | 68 <expand macro="citations" /> |
69 </tool> |