Mercurial > repos > iuc > gemini_mendel_errors

annotate gemini_mendel_errors.xml @ 0:886fdfe90b01 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
author iuc
date Tue, 16 Feb 2016 05:53:45 -0500
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children 453eb01e00e7
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886fdfe90b01 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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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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14 #if $report.report_selector != 'all':
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15 --columns "${report.columns}"
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16 #end if
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18 @CMDLN_SQL_FILTER_FILTER_OPTION@
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20 #if int($min_kindreds) > 0:
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21 --min-kindreds $min_kindreds
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22 #end if
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24 #if str($families).strip():
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25 --families "$families"
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26 #end if
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27
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28 $lenient
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29 $only_affected
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31 -d $d
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32
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33 #if int($min_gq) > 0:
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34 --min-gq $min_gq
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35 #end if
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37 #if int($gt_pl_max) > -1:
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38 --gt-pl-max $gt_pl_max
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39 #end if
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41
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42 "${ infile }"
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43 > "${ outfile }"
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44 ]]>
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45 </command>
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46 <inputs>
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47 <expand macro="infile" />
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48 <expand macro="column_filter" />
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49 <expand macro="filter" />
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50 <expand macro="min_kindreds" />
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51 <expand macro="family" />
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52 <expand macro="lenient" />
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53 <!-- this parameter should be allow-unaffected, but unfortunately it is not. -->
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54 <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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55 <expand macro="min_sequence_depth" />
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56 <expand macro="min_gq" />
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57 <expand macro="gt_pl_max" />
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58 </inputs>
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59 <outputs>
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60 <data name="outfile" format="tabular" />
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
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65 <param name="columns" value="gene,ref,alt,impact" />
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66 <output name="outfile" file="gemini_mendel_errors_result.tabular" />
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67 </test>
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68 </tests>
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69 <help>
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70 <![CDATA[
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71
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72 **What it does**
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73
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74 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI,
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75 you can use this tool for identifying mutations that violate the Mendelian inheritance scheme.
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76
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77 ]]>
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78 </help>
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79 <expand macro="citations"/>
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80 </tool>