Mercurial > repos > iuc > gemini_qc

annotate gemini_qc.xml @ 8:20f2ecf46dcb draft default tip

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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 15:25:17 +0000
parents 8414eecc3828
children
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8414eecc3828 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@">
0
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2 <description>Quality control tool</description>
8
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3 <expand macro="bio_tools"/>
0
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4 <macros>
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5 <import>gemini_macros.xml</import>
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6 <token name="@BINARY@">qc</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[
a875f940d8fd 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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14 --mode sex
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8414eecc3828 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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15 --chrom '$chrom'
0
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16
5
8414eecc3828 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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17 '$infile'
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18 > '$outfile'
0
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19 ]]>
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20 </command>
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21 <inputs>
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22 <expand macro="infile" />
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23 <param name="chrom" type="text" value="chrX" label="Which chromosome should the sex test be applied to?" help="(--chrom)"/>
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24
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25 </inputs>
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26 <outputs>
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27 <data name="outfile" format="tabular" />
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28 </outputs>
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29 <tests>
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30 <test>
4
246ad1a7ff20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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31 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
246ad1a7ff20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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32 <!-- Testing needs to be done on a chromsome that exists
246ad1a7ff20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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33 in the test database even if that has little biological meaning
246ad1a7ff20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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34 -->
246ad1a7ff20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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35 <param name="chrom" value="chr1" ftype="gemini.sqlite" />
246ad1a7ff20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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36 <output name="outfile">
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37 <assert_contents>
246ad1a7ff20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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38 <has_line_matching expression="sample&#009;sex&#009;.*" />
246ad1a7ff20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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39 </assert_contents>
246ad1a7ff20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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40 </output>
0
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41 </test>
a875f940d8fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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42 </tests>
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43 <help>
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44 <![CDATA[
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45 **What it does**
a875f940d8fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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46
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47 Checks whether the given sex of the samples are probable. It issues the query::
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48
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49 SELECT gt_types
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50 FROM variants
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51 WHERE chrom = '$chrom'
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52 AND start > 2699520 and start < 154931044
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53 AND call_rate > 0.90
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54 AND depth > 1000
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55 AND filter is NULL
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56 ORDER BY random()
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57 LIMIT 10000
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58
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59 and returns the called variants on that region of the given chromosome in a table::
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60
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61 sample sex X_homref X_het X_homalt het_homref_ratio
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62 SMS173 male 7265 1975 8010 0.271851342051
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63 SMS254 male 5440 1316 3846 0.241911764706
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64 SMS255 female 6275 3188 5423 0.508047808765
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65 SMS253 male 5536 1355 3582 0.244761560694
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66 SMS243 male 6181 1506 4479 0.243649894839
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67 SMS242 male 6365 1437 4200 0.225765907306
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68 SMS193 male 6667 1864 5829 0.279586020699
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69 SMS238 male 6263 1638 4891 0.261536005109
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70 SMS239 female 6755 3669 7618 0.543153219837
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71 SMS244 female 6489 2953 5140 0.45507782401
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72 SMS230 male 7209 1784 7146 0.247468442225
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73 SMS231 female 7306 4659 9332 0.637695045168
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74 ]]>
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75
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76 </help>
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77 <expand macro="citations"/>
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78 </tool>