Mercurial > repos > iuc > gemini_set_somatic

annotate gemini_set_somatic.xml @ 1:eae49d42a4a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:36:16 -0500
parents 5245c281db29
children bd723bd67a67
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
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2 <description>Tag somatic mutations in a GEMINI database</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@">set_somatic</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[
1
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12 @PROVIDE_ANNO_DATA@
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13
0
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14 cp "${ infile }" "${ outfile }" &&
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16 gemini @BINARY@
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18 #if float($min_depth) >= 0:
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19 --min-depth $min_depth
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20 #end if
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22 #if float($min_quality) >= 0:
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23 --min-qual $min_quality
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24 #end if
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26 #if float($min_somatic_score) >= 0:
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27 --min-somatic-score $min_somatic_score
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28 #end if
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30 #if float($max_norm_alt_freq) >= 0:
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31 --max-norm-alt-freq $max_norm_alt_freq
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32 #end if
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34 #if int($max_norm_alt_count) >= 0:
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35 --max-norm-alt-count $max_norm_alt_count
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36 #end if
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38 #if int($min_norm_depth) >= 0:
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39 --min-norm-depth $min_norm_depth
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40 #end if
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42 #if float($min_tumor_alt_freq) >= 0:
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43 --min-tumor-alt-freq $min_tumor_alt_freq
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44 #end if
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46 #if int($min_tumor_alt_count) >= 0:
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47 --min-tumor-alt-count $min_tumor_alt_count
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48 #end if
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49
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50 #if int($min_tumor_depth) >= 0:
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51 --min-tumor-depth $min_tumor_depth
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52 #end if
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53
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54 #if str($chrom).strip():
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55 --chrom "$chrom"
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56 #end if
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57 "${ outfile }"
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58 ]]>
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59 </command>
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60 <inputs>
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61
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62 <expand macro="infile" />
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63 <param name="min_depth" type="float" value="-1" label="The min combined depth for tumor + normal" help="default: -1 (not set) (--min-depth)"/>
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64 <param name="min_quality" type="float" value="-1" label="The min variant quality (VCF QUAL)" help="default: -1 (not set) (--min-qual)"/>
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65 <param name="min_somatic_score" type="float" value="-1" label="The min somatic score (SSC)" help="default: -1 (not set) (--min-somatic-score)"/>
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66 <param name="max_norm_alt_freq" type="float" value="-1" label="The max frequency of the alternative allele in the normal sample" help="default: -1 (not set) (--max-norm-alt-freq)"/>
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67 <param name="max_norm_alt_count" type="integer" value="-1" min="-1" label="The max count of the alternative allele in the normal sample" help="default: -1 (not set) (--max-norm-alt-count)"/>
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68 <param name="min_norm_depth" type="integer" value="-1" min="-1" label="The minimum depth allowed in the normal sample to believe somatic" help="default: -1 (not set) (--min-norm-depth)"/>
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69 <param name="min_tumor_alt_freq" type="float" value="-1" label="The minimum frequency of the alternative allele in the tumor sample" help="default: -1 (not set) (--min-tumor-alt-freq)"/>
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70 <param name="min_tumor_alt_count" type="integer" value="-1" min="-1" label="The minimum count of the alternative allele in the tumor sample" help="default: -1 (not set) (--min-tumor-alt-count)"/>
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71 <param name="min_tumor_depth" type="integer" value="-1" min="-1" label="The minimum depth allowed in the tumor sample to believe somatic" help="default: -1 (not set) (--min-tumor-depth)"/>
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72 <param name="chrom" type="text" label="A specific chromosome on which to tag somatic mutations" help="e.g. chrom12 (--chrom)" />
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73
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74 </inputs>
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75 <outputs>
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76 <data name="outfile" format="gemini.sqlite" />
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77 </outputs>
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78 <tests>
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79 <test>
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80 <!-- A very basic test with a nonsensical input db. The example
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81 databases that would produce something meaningful are >100 Mbyte -->
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82 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
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83 <param name="min_somatic_score" value="5.65" />
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84 <output name="outfile" file="gemini_is_somatic_result.db" />
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85 </test>
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86 </tests>
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87 <help>
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88 <![CDATA[
5245c281db29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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89 **What it does**
5245c281db29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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90
5245c281db29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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91 Gemini set_somatic sets the flag "is_somatic" by comparing tumor/normal pairs in an already loaded Gemini database.
5245c281db29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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92
5245c281db29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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93 ]]>
5245c281db29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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94 </help>
5245c281db29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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95 <expand macro="citations"/>
5245c281db29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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96 </tool>