Mercurial > repos > iuc > bedtools
annotate bedpeToBam.xml @ 35:b28e0cfa7ba1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
author | iuc |
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date | Fri, 06 Sep 2019 14:29:59 -0400 |
parents | dde39ba9c031 |
children | 3e38c9b3214f |
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@"> |
4
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> | |
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b28e0cfa7ba1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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changeset
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6 <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> --> |
b28e0cfa7ba1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
34
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changeset
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7 <requirements> |
b28e0cfa7ba1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
34
diff
changeset
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8 <requirement type="package" version="2.27.1">bedtools</requirement> |
b28e0cfa7ba1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
34
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changeset
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9 </requirements> |
0 | 10 <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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11 <command><![CDATA[ |
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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12 bedtools bedpetobam |
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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13 -mapq $mapq |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
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changeset
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14 -i '$input' |
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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15 -g @GENOME_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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16 > '$output' |
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 ]]></command> |
0 | 18 <inputs> |
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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19 <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:
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diff
changeset
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20 <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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21 <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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22 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" /> |
0 | 23 </inputs> |
24 <outputs> | |
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b28e0cfa7ba1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
34
diff
changeset
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25 <data name="output" format="unsorted.bam" metadata_source="input"/> |
0 | 26 </outputs> |
1 | 27 <tests> |
28 <test> | |
29 <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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30 <param name="genome_file_opts_selector" value="hist" /> |
1 | 31 <param name="genome" value="mm9.len"/> |
35
b28e0cfa7ba1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
34
diff
changeset
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32 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="unsorted.bam" /> |
1 | 33 </test> |
34 </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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35 <help><![CDATA[ |
0 | 36 **What it does** |
37 | |
38 Converts feature records to BAM format. | |
39 | |
40 .. class:: warningmark | |
41 | |
42 BED files must be at least BED4 to create BAM (needs name field). | |
43 | |
44 @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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45 ]]></help> |
0 | 46 <expand macro="citations" /> |
47 </tool> |