Mercurial > repos > iuc > gemini_lof_sieve
comparison gemini_lof_sieve.xml @ 0:be7ac09bc2fa draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
| author | iuc |
|---|---|
| date | Thu, 18 Feb 2016 08:53:32 -0500 |
| parents | |
| children | 93a391b4602c |
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| -1:000000000000 | 0:be7ac09bc2fa |
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| 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> | |
| 2 <description>Filter LoF variants by transcript position and type</description> | |
| 3 <macros> | |
| 4 <import>gemini_macros.xml</import> | |
| 5 <token name="@BINARY@">lof_sieve</token> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <expand macro="stdio" /> | |
| 9 <expand macro="version_command" /> | |
| 10 <command> | |
| 11 <![CDATA[ | |
| 12 gemini @BINARY@ | |
| 13 "${ infile }" | |
| 14 > "${ outfile }" | |
| 15 ]]> | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <expand macro="infile" /> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data name="outfile" format="tabular" /> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test> | |
| 25 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" /> | |
| 26 <output name="outfile" file="gemini_lofsieve_result.tabular" /> | |
| 27 </test> | |
| 28 </tests> | |
| 29 <help><![CDATA[ | |
| 30 **What it does** | |
| 31 | |
| 32 *Filter LoF variants by transcript position and type* | |
| 33 | |
| 34 Not all candidate LoF variants are created equal. For e.g, a nonsense (stop gain) variant impacting the first 5% of a polypeptide is far | |
| 35 more likely to be deleterious than one affecting the last 5%. Assuming you’ve annotated your VCF with snpEff v3.0+, the lof_sieve tool | |
| 36 reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence. | |
| 37 In addition, it also reports the predicted function of the transcript so that one can segregate candidate | |
| 38 LoF variants that affect protein_coding transcripts from processed RNA, etc. | |
| 39 | |
| 40 **Example** | |
| 41 | |
| 42 Output with default settings:: | |
| 43 | |
| 44 chrom start end ref alt highest_impact aa_change var_trans_pos trans_aa_length var_trans_pct sample genotype gene transcript trans_type | |
| 45 chr22 17072346 17072347 C T stop_gain W365* 365 557 0.655296229803 NA19327 C|T CCT8L2 ENST00000359963 protein_coding | |
| 46 chr22 17072346 17072347 C T stop_gain W365* 365 557 0.655296229803 NA19375 T|C CCT8L2 ENST00000359963 protein_coding | |
| 47 chr22 17129539 17129540 C T splice_donor None None None None NA18964 T|C TPTEP1 ENST00000383140 lincRNA | |
| 48 chr22 17129539 17129540 C T splice_donor None None None None NA19675 T|C TPTEP1 ENST00000383140 lincRNA | |
| 49 | |
| 50 ]]></help> | |
| 51 <expand macro="citations"/> | |
| 52 </tool> |