Mercurial > repos > iuc > bedtools
annotate bedpeToBam.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author | iuc |
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date | Mon, 29 Apr 2019 05:55:48 -0400 |
parents | 4f7a5ccd2ae9 |
children | b28e0cfa7ba1 |
rev | line source |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
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changeset
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1 <tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" 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>converter</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
parents:
32
diff
changeset
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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:
32
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changeset
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9 bedtools bedpetobam |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
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changeset
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10 -mapq $mapq |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
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changeset
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11 -i '$input' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
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changeset
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12 -g @GENOME_FILE@ |
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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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> |
34
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="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
4
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changeset
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17 <expand macro="input_conditional_genome_file" /> |
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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18 <param argument="-mapq" type="integer" value="255" |
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="Set a mapping quality (SAM MAPQ field) value for all BED entries" /> |
0 | 20 </inputs> |
21 <outputs> | |
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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22 <data name="output" format="bam" metadata_source="input"/> |
0 | 23 </outputs> |
1 | 24 <tests> |
25 <test> | |
26 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" /> | |
17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
4
diff
changeset
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27 <param name="genome_file_opts_selector" value="hist" /> |
1 | 28 <param name="genome" value="mm9.len"/> |
29 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" /> | |
30 </test> | |
31 </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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32 <help><![CDATA[ |
0 | 33 **What it does** |
34 | |
35 Converts feature records to BAM format. | |
36 | |
37 .. class:: warningmark | |
38 | |
39 BED files must be at least BED4 to create BAM (needs name field). | |
40 | |
41 @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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42 ]]></help> |
0 | 43 <expand macro="citations" /> |
44 </tool> |