Mercurial > repos > iuc > gemini_lof_sieve

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:26:20 +0000
parents dda378a72430
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dda378a72430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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2 <description>Filter LoF variants by transcript position and type</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>gemini_macros.xml</import>
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6 <token name="@BINARY@">lof_sieve</token>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
be7ac09bc2fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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13 gemini @BINARY@
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dda378a72430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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14 '$infile'
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15 > '$outfile'
0
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16 ]]>
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17 </command>
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18 <inputs>
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19 <expand macro="infile" />
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20 </inputs>
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21 <outputs>
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22 <data name="outfile" format="tabular" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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27 <output name="outfile">
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28 <assert_contents>
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29 <has_line_matching expression="chrom&#009;start&#009;end&#009;.*highest_impact.*" />
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30 </assert_contents>
93a391b4602c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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31 </output>
0
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 **What it does**
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37 *Filter LoF variants by transcript position and type*
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38
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39 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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40 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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41 reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence.
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42 In addition, it also reports the predicted function of the transcript so that one can segregate candidate
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43 LoF variants that affect protein_coding transcripts from processed RNA, etc.
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45 **Example**
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47 Output with default settings::
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49 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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50 chr22 17072346 17072347 C T stop_gain W365* 365 557 0.655296229803 NA19327 C|T CCT8L2 ENST00000359963 protein_coding
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51 chr22 17072346 17072347 C T stop_gain W365* 365 557 0.655296229803 NA19375 T|C CCT8L2 ENST00000359963 protein_coding
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52 chr22 17129539 17129540 C T splice_donor None None None None NA18964 T|C TPTEP1 ENST00000383140 lincRNA
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53 chr22 17129539 17129540 C T splice_donor None None None None NA19675 T|C TPTEP1 ENST00000383140 lincRNA
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54
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55 ]]></help>
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56 <expand macro="citations"/>
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57 </tool>