Mercurial > repos > iuc > bedtools
annotate bedpeToBam.xml @ 32:b0d5e752c0c5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
| author | iuc |
|---|---|
| date | Tue, 05 Sep 2017 09:51:56 -0400 |
| parents | a2d4c30ba2f9 |
| children | ac2040a5e6ff |
| rev | line source |
|---|---|
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
17
diff
changeset
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1 <tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.1"> |
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17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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2 <description>converter</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools bedpetobam | |
| 11 -mapq $mapq | |
| 12 -i '$input' | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
17
diff
changeset
|
13 -g @GENOME_FILE@ |
| 8 | 14 > '$output' |
| 15 ]]> | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
17
diff
changeset
|
19 <expand macro="input_conditional_genome_file" /> |
| 8 | 20 <param name="mapq" type="integer" value="255" |
| 21 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" | |
| 22 help="(-mapq)" /> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data format="bam" name="output" metadata_source="input"/> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test> | |
| 29 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" /> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
17
diff
changeset
|
30 <param name="genome_file_opts_selector" value="hist" /> |
| 8 | 31 <param name="genome" value="mm9.len"/> |
| 32 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" /> | |
| 33 </test> | |
| 34 </tests> | |
| 35 <help> | |
| 36 <![CDATA[ | |
| 37 **What it does** | |
| 38 | |
| 39 Converts feature records to BAM format. | |
| 40 | |
| 41 .. class:: warningmark | |
| 42 | |
| 43 BED files must be at least BED4 to create BAM (needs name field). | |
| 44 | |
| 45 @REFERENCES@ | |
| 46 ]]> | |
| 47 </help> | |
| 48 <expand macro="citations" /> | |
| 49 </tool> |