Mercurial > repos > iuc > gemini_mendel_errors

annotate gemini_mendel_errors.xml @ 3:083ddae3ec8b 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 12:27:11 -0500
parents 58899bab0641
children 0b3171d548a2
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
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2 <description>Identify candidate violations of Mendelian inheritance</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@">mendel_errors</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
1
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14 @COLUMN_SELECT@
0
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16 @CMDLN_SQL_FILTER_FILTER_OPTION@
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18 #if int($min_kindreds) > 0:
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19 --min-kindreds $min_kindreds
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20 #end if
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22 #if str($families).strip():
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23 --families "$families"
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24 #end if
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26 $lenient
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27 $only_affected
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29 -d $d
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31 #if int($min_gq) > 0:
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32 --min-gq $min_gq
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33 #end if
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35 #if int($gt_pl_max) > -1:
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36 --gt-pl-max $gt_pl_max
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37 #end if
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40 "${ infile }"
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41 > "${ outfile }"
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42 ]]>
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43 </command>
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44 <inputs>
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45 <expand macro="infile" />
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46 <expand macro="column_filter" />
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47 <expand macro="filter" />
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48 <expand macro="min_kindreds" />
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49 <expand macro="family" />
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50 <expand macro="lenient" />
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51 <!-- this parameter should be allow-unaffected, but unfortunately it is not. -->
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52 <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False" label="Only consider candidates from affected samples." help="(--only-affected)"/>
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53 <expand macro="min_sequence_depth" />
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54 <expand macro="min_gq" />
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55 <expand macro="gt_pl_max" />
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56 </inputs>
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57 <outputs>
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58 <data name="outfile" format="tabular" />
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
3
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63 <conditional name="report">
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64 <param name="report_selector" value="column_filter" />
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65 <param name="columns" value="gene,ref,alt,impact" />
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66 </conditional>
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67 <output name="outfile">
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68 <assert_contents>
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69 <has_line_matching expression="gene&#009;ref&#009;alt&#009;impact&#009;.*violation.*" />
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70 </assert_contents>
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71 </output>
0
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72 </test>
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73 </tests>
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74 <help>
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75 <![CDATA[
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76
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77 **What it does**
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78
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79 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI,
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80 you can use this tool for identifying mutations that violate the Mendelian inheritance scheme.
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81
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82 ]]>
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83 </help>
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84 <expand macro="citations"/>
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85 </tool>