Mercurial > repos > iuc > gemini_lof_sieve

annotate gemini_lof_sieve.xml @ 4:93a391b4602c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:48:41 -0500
parents be7ac09bc2fa
children dda378a72430
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93a391b4602c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
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2 <description>Filter LoF variants by transcript position and type</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">lof_sieve</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 gemini @BINARY@
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13 "${ infile }"
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14 > "${ outfile }"
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15 ]]>
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16 </command>
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17 <inputs>
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18 <expand macro="infile" />
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19 </inputs>
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20 <outputs>
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21 <data name="outfile" format="tabular" />
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22 </outputs>
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23 <tests>
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24 <test>
4
93a391b4602c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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25 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
93a391b4602c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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26 <output name="outfile">
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27 <assert_contents>
93a391b4602c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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28 <has_line_matching expression="chrom&#009;start&#009;end&#009;.*highest_impact.*" />
93a391b4602c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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29 </assert_contents>
93a391b4602c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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30 </output>
0
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 **What it does**
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35
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36 *Filter LoF variants by transcript position and type*
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37
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38 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
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39 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
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40 reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence.
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41 In addition, it also reports the predicted function of the transcript so that one can segregate candidate
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42 LoF variants that affect protein_coding transcripts from processed RNA, etc.
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43
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44 **Example**
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45
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46 Output with default settings::
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47
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48 chrom start end ref alt highest_impact aa_change var_trans_pos trans_aa_length var_trans_pct sample genotype gene transcript trans_type
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49 chr22 17072346 17072347 C T stop_gain W365* 365 557 0.655296229803 NA19327 C|T CCT8L2 ENST00000359963 protein_coding
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50 chr22 17072346 17072347 C T stop_gain W365* 365 557 0.655296229803 NA19375 T|C CCT8L2 ENST00000359963 protein_coding
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51 chr22 17129539 17129540 C T splice_donor None None None None NA18964 T|C TPTEP1 ENST00000383140 lincRNA
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52 chr22 17129539 17129540 C T splice_donor None None None None NA19675 T|C TPTEP1 ENST00000383140 lincRNA
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53
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54 ]]></help>
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55 <expand macro="citations"/>
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56 </tool>