Mercurial > repos > iuc > gemini_lof_sieve

annotate gemini_lof_sieve.xml @ 2:9511c648d044 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 13:15:36 -0500
parents be7ac09bc2fa
children 93a391b4602c
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be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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2 <description>Filter LoF variants by transcript position and type</description>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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3 <macros>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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4 <import>gemini_macros.xml</import>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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5 <token name="@BINARY@">lof_sieve</token>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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9 <expand macro="version_command" />
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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10 <command>
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11 <![CDATA[
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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12 gemini @BINARY@
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13 "${ infile }"
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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14 > "${ outfile }"
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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15 ]]>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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16 </command>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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17 <inputs>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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18 <expand macro="infile" />
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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19 </inputs>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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20 <outputs>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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21 <data name="outfile" format="tabular" />
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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22 </outputs>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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23 <tests>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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24 <test>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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25 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
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26 <output name="outfile" file="gemini_lofsieve_result.tabular" />
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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27 </test>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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28 </tests>
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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29 <help><![CDATA[
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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30 **What it does**
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31
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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32 *Filter LoF variants by transcript position and type*
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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33
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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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
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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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
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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36 reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence.
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37 In addition, it also reports the predicted function of the transcript so that one can segregate candidate
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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38 LoF variants that affect protein_coding transcripts from processed RNA, etc.
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39
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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40 **Example**
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be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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42 Output with default settings::
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43
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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
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45 chr22 17072346 17072347 C T stop_gain W365* 365 557 0.655296229803 NA19327 C|T CCT8L2 ENST00000359963 protein_coding
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46 chr22 17072346 17072347 C T stop_gain W365* 365 557 0.655296229803 NA19375 T|C CCT8L2 ENST00000359963 protein_coding
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47 chr22 17129539 17129540 C T splice_donor None None None None NA18964 T|C TPTEP1 ENST00000383140 lincRNA
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48 chr22 17129539 17129540 C T splice_donor None None None None NA19675 T|C TPTEP1 ENST00000383140 lincRNA
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49
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50 ]]></help>
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51 <expand macro="citations"/>
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52 </tool>