Mercurial > repos > devteam > vcfcombine
annotate vcfcombine.xml @ 1:55ca04702702 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:58:45 -0500 |
| parents | da419f5ed589 |
| children | 18f9f2624bd6 |
| rev | line source |
|---|---|
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55ca04702702
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
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changeset
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1 <tool id="vcfcombine" name="VCFcombine:" version="0.0.4"> |
| 0 | 2 <description>Combine multiple VCF datasets</description> |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"></expand> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 | |
| 10 vcfcombine | |
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55ca04702702
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
11 |
| 0 | 12 #for $input_vcf in $input_vcfs: |
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55ca04702702
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
13 "${input_vcf}" |
| 0 | 14 #end for |
| 15 | |
| 16 > "${out_file1}" | |
| 17 | |
| 18 </command> | |
| 19 <inputs> | |
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1
55ca04702702
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
20 <param name="input_vcfs" type="data" format="vcf" label="Select VCF Datasets" min="2" multiple="True"/> |
| 0 | 21 </inputs> |
| 22 <outputs> | |
| 23 <data format="vcf" name="out_file1" /> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
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1
55ca04702702
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
27 <param name="input_vcfs" value="vcflib.vcf"/> |
| 0 | 28 <output name="out_file1" file="vcfcombine-test1.vcf"/> |
| 29 </test> | |
| 30 </tests> | |
| 31 <help> | |
| 32 | |
| 33 Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files, which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted. | |
| 34 | |
| 35 ----- | |
| 36 | |
| 37 Vcfcombine @IS_PART_OF_VCFLIB@ | |
| 38 </help> | |
| 39 <expand macro="citations" /> | |
| 40 </tool> |