Mercurial > repos > iuc > gemini
annotate gemini_comp_hets.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 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> |
| 2 <description>Identifying potential compound heterozygotes</description> | |
| 3 <macros> | |
| 4 <import>gemini_macros.xml</import> | |
| 5 <token name="@BINARY@">comp_hets</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 | |
| 14 #if $report.report_selector != 'all': | |
| 15 --columns "${report.columns}" | |
| 16 #end if | |
| 17 | |
| 11 | 18 @CMDLN_SQL_FILTER_FILTER_OPTION@ |
| 19 | |
| 0 | 20 $only_affected |
| 21 $ignore_phasing | |
| 22 | |
| 23 "${ infile }" | |
| 24 > "${ outfile }" | |
| 25 ]]> | |
| 26 </command> | |
| 27 <inputs> | |
| 11 | 28 <expand macro="infile" /> |
| 0 | 29 <expand macro="add_header_column" /> |
| 2 | 30 <expand macro="column_filter" /> |
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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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31 <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False" |
| 0 | 32 label="Report solely those compund heterozygotes impacted a sample labeled as affected" help="(--only-affected)"/> |
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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
|
33 <param name="ignore_phasing" type="boolean" truevalue="--ignore-phasing" falsevalue="" checked="False" |
| 0 | 34 label="Ignore phasing when screening for compound hets" help="Candidates are inherently putative. (--ignore-phasing)"/> |
| 35 <expand macro="filter" /> | |
| 36 </inputs> | |
| 37 <outputs> | |
| 11 | 38 <data name="outfile" format="tabular" /> |
| 0 | 39 </outputs> |
| 40 <tests> | |
| 41 <test> | |
| 42 </test> | |
| 43 </tests> | |
| 44 <help> | |
| 45 **What it does** | |
| 46 | |
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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 Many recessive disorders are caused by compound heterozygotes. Unlike canonical recessive sites where the same recessive allele is |
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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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48 inherited from both parents at the _same_ site in the gene, compound heterozygotes occur when the individual’s phenotype is caused |
| 0 | 49 by two heterozygous recessive alleles at _different_ sites in a particular gene. |
| 50 | |
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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
|
51 So basically, we are looking for two (typically loss-of-function (LoF)) heterozygous variants impacting the same gene at different loci. |
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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
|
52 The complicating factor is that this is _recessive_ and as such, we must also require that the consequential alleles at each heterozygous |
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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
|
53 site were inherited on different chromosomes (one from each parent). As such, in order to use this tool, we require that all variants are phased. |
| 0 | 54 Once this has been done, the comp_hets tool will provide a report of candidate compound heterozygotes for each sample/gene. |
| 55 | |
| 56 | |
| 57 @CITATION@ | |
| 58 </help> | |
| 59 <expand macro="citations"/> | |
| 60 </tool> |