Mercurial > repos > iuc > gemini_set_somatic

annotate gemini_set_somatic.xml @ 6:3208dd1dbfe2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 251c6024b4ff643a63e17fbfe2590998c2bae3a7"
author iuc
date Fri, 24 Jan 2020 17:39:33 -0500
parents 991049484627
children 7814e39409d1
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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[
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12 cp '$infile' '$outfile' &&
0
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14 gemini @BINARY@
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16 #if float($min_depth) >= 0:
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17 --min-depth $min_depth
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18 #end if
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20 #if float($min_quality) >= 0:
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21 --min-qual $min_quality
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22 #end if
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24 #if float($min_somatic_score) >= 0:
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25 --min-somatic-score $min_somatic_score
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26 #end if
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28 #if float($max_norm_alt_freq) >= 0:
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29 --max-norm-alt-freq $max_norm_alt_freq
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30 #end if
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32 #if int($max_norm_alt_count) >= 0:
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33 --max-norm-alt-count $max_norm_alt_count
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34 #end if
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36 #if int($min_norm_depth) >= 0:
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37 --min-norm-depth $min_norm_depth
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38 #end if
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40 #if float($min_tumor_alt_freq) >= 0:
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41 --min-tumor-alt-freq $min_tumor_alt_freq
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42 #end if
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44 #if int($min_tumor_alt_count) >= 0:
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45 --min-tumor-alt-count $min_tumor_alt_count
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46 #end if
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48 #if int($min_tumor_depth) >= 0:
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49 --min-tumor-depth $min_tumor_depth
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50 #end if
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52 #if str($chrom).strip():
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53 --chrom '$chrom'
0
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54 #end if
5
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55 '$outfile'
0
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56 ]]>
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57 </command>
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58 <inputs>
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59
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60 <expand macro="infile" />
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61 <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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62 <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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63 <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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64 <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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65 <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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66 <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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67 <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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68 <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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69 <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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70 <param name="chrom" type="text" label="A specific chromosome on which to tag somatic mutations" help="e.g. chrom12 (--chrom)" />
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71
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72 </inputs>
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73 <outputs>
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74 <data name="outfile" format="gemini.sqlite" />
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75 </outputs>
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76 <tests>
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77 <test>
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78 <!-- A very basic test with a nonsensical input db. The example
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79 databases that would produce something meaningful are >100 Mbyte -->
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80 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
0
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81 <param name="min_somatic_score" value="5.65" />
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82 <output name="outfile" file="gemini_is_somatic_result.db" />
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83 </test>
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84 </tests>
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85 <help>
230c975e7759 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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86 <![CDATA[
230c975e7759 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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87 **What it does**
230c975e7759 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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88
230c975e7759 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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89 Gemini set_somatic sets the flag "is_somatic" by comparing tumor/normal pairs in an already loaded Gemini database.
230c975e7759 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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90
230c975e7759 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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91 ]]>
230c975e7759 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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92 </help>
230c975e7759 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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93 <expand macro="citations"/>
230c975e7759 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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94 </tool>