Mercurial > repos > iuc > gemini
annotate gemini_burden.xml @ 17:65f742e605ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:46:38 -0400 |
| parents | 53a5647e5271 |
| children | ce61d4876838 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> |
| 2 <description>perform sample-wise gene-level burden calculations</description> | |
| 3 <macros> | |
| 4 <import>gemini_macros.xml</import> | |
| 5 <token name="@BINARY@">burden</token> | |
| 6 </macros> | |
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65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
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7 <expand macro="requirements" /> |
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65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
8 <expand macro="stdio" /> |
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65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
9 <expand macro="version_command" /> |
| 0 | 10 <command> |
| 11 <![CDATA[ | |
| 12 gemini @BINARY@ | |
| 13 --cases $cases | |
| 14 --controls $controls | |
| 15 $save_tscores | |
| 16 $nonsynonymous | |
| 17 $calpha | |
| 18 --permutations $permutations | |
| 8 | 19 #if float( str($min_aaf) ) >= 0.0: |
| 0 | 20 --min-aaf $min_aaf |
| 21 #end if | |
| 8 | 22 #if float( str($max_aaf) ) >= 0.0: |
| 0 | 23 --max-aaf $max_aaf |
| 24 #end if | |
| 25 "${ infile }" | |
| 26 > "${ outfile }" | |
| 27 ]]> | |
| 28 | |
| 29 </command> | |
| 30 <inputs> | |
| 11 | 31 <expand macro="infile" /> |
| 0 | 32 |
| 33 <param name="cases" size="30" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/> | |
| 34 <param name="controls" size="30" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/> | |
| 35 | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
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36 <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False" |
| 0 | 37 label="Save the permuted T-scores in the output file" help="(--save_tscores)"/> |
| 38 | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
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39 <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False" |
| 0 | 40 label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/> |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
41 <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False" |
| 0 | 42 label="Run the C-alpha association test" help="(--calpha)"/> |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
43 <param name="min_aaf" type="float" value="-1" size="5" label="The min. alt. allele frequency for a variant to be included" |
| 0 | 44 help="(--min-aaf)"> |
| 2 | 45 <!--validator type="in_range" min="0.0"/--> |
| 0 | 46 </param> |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
47 <param name="max_aaf" type="float" value="-1" size="5" label="The max. alt. allele frequency for a variant to be included" |
| 0 | 48 help="(--max-aaf)"> |
| 2 | 49 <!--validator type="in_range" min="0.0"/--> |
| 0 | 50 </param> |
| 51 | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
52 <param name="permutations" type="integer" value="1000" size="10" label="Number of permutations to run for the C-alpha test" |
| 0 | 53 help="(--permutations)"> |
| 54 <validator type="in_range" min="0"/> | |
| 55 </param> | |
| 56 | |
| 57 </inputs> | |
| 58 <outputs> | |
| 11 | 59 <data name="outfile" format="tabular" /> |
| 0 | 60 </outputs> |
| 61 <tests> | |
| 62 <test> | |
| 63 </test> | |
| 64 </tests> | |
| 65 <help> | |
| 66 **What it does** | |
| 67 | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
68 The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis. |
| 0 | 69 By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample. |
| 70 | |
| 71 $ gemini burden test.burden.db | |
| 72 gene M10475 M10478 M10500 M128215 | |
| 73 WDR37 2 2 2 2 | |
| 74 CTBP2 0 0 0 1 | |
| 75 DHODH 1 0 0 0 | |
| 76 | |
| 77 @CITATION@ | |
| 78 </help> | |
| 79 <expand macro="citations"> | |
| 80 <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation --> | |
| 81 </expand> | |
| 82 </tool> |