Mercurial > repos > jjohnson > snpeff_cds_report
annotate snpEff_cds_report.xml @ 7:fbb6510186df default tip
when codon has ambiguous nucleotide translate to X
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 15 Sep 2014 06:13:47 -0500 |
| parents | 85b933b7d231 |
| children |
| rev | line source |
|---|---|
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85b933b7d231
Make the reporting of the SnpEff Amino_Acid_change field an option
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
|
1 <tool id="SnpEff-cds-report" name="SnpEff Ensembl CDS" version="1.2"> |
| 0 | 2 <description>Report Variant coding sequence changes for SnpEffects</description> |
| 3 <command interpreter="python"> | |
| 4 snpEff_cds_report.py --in $snp_effect_vcf | |
| 5 #if len($ensembl_host.__str__.strip) > 0: | |
| 6 --ensembl_host ${ensembl_host}.archive.ensembl.org | |
| 7 #end if | |
| 8 #if len($ensembl_dataset.__str__.strip) > 0: | |
| 9 --ensembl_dataset $ensembl_dataset | |
| 10 #end if | |
| 11 #if len($polya.__str__.strip) > 0: | |
| 12 --polyA_limit $polya | |
| 13 #end if | |
| 14 #if $effects_filter | |
| 15 --effects_filter=$effects_filter | |
| 16 #end if | |
| 17 $all_effects | |
| 18 $with_ccds | |
|
5
85b933b7d231
Make the reporting of the SnpEff Amino_Acid_change field an option
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
|
19 $snpeff_aa_change |
| 0 | 20 #if $report_format.__str__.find('html') >= 0: |
| 21 --html_report $html_report | |
| 22 --html_dir $html_report.extra_files_path | |
| 23 #end if | |
| 24 #if $report_format.__str__.find('tsv') >= 0: | |
| 25 --tsv_file $tsv_report | |
| 26 #end if | |
| 27 #if $report_format.__str__.find('detailed') >= 0: | |
| 28 --out $text_report | |
| 29 #end if | |
| 30 </command> | |
| 31 <inputs> | |
| 32 <param name="snp_effect_vcf" type="data" format="vcf" label="SnpEffect VCF report" help="VCF output from SnpEffect or SnpSift"/> | |
| 33 <param name="ensembl_host" type="text" value="" label="Biomart Server (defaults to www.biomart.org, for an archive server enter the archive date)" help="feb2012 - would access ensembl server: feb2012.archive.ensembl.org"> | |
| 34 <validator type="regex" message="format: mmmYYYY">^([jfmajsond][aepuco][nbrynlgptvc]20[0-9][0-9])?$</validator> | |
| 35 </param> | |
| 36 <param name="ensembl_dataset" type="select" label="Oragnism" help=""> | |
| 37 <option value="hsapiens_gene_ensembl" selected="true">Homo sapiens</option> | |
| 38 <option value="mmusculus_gene_ensembl">Mus musculus</option> | |
| 39 <option value="rnorvegicus_gene_ensembl">Rattus norvegicus</option> | |
| 40 <option value="drerio_gene_ensembl">Danio rerio</option> | |
| 41 <option value="ggallus_gene_ensembl">Gallus gallus</option> | |
| 42 <option value="amelanoleuca_gene_ensembl">Ailuropoda melanoleuca</option> | |
| 43 <option value="acarolinensis_gene_ensembl">Anolis carolinensis</option> | |
| 44 <option value="btaurus_gene_ensembl">Bos taurus</option> | |
| 45 <option value="celegans_gene_ensembl">Caenorhabditis elegans</option> | |
| 46 <option value="cjacchus_gene_ensembl">Callithrix jacchus</option> | |
| 47 <option value="cfamiliaris_gene_ensembl">Canis familiaris</option> | |
| 48 <option value="cporcellus_gene_ensembl">Cavia porcellus</option> | |
| 49 <option value="choffmanni_gene_ensembl">Choloepus hoffmanni</option> | |
| 50 <option value="cintestinalis_gene_ensembl">Ciona intestinalis</option> | |
| 51 <option value="csavignyi_gene_ensembl">Ciona savignyi</option> | |
| 52 <option value="dnovemcinctus_gene_ensembl">Dasypus novemcinctus</option> | |
| 53 <option value="dordii_gene_ensembl">Dipodomys ordii</option> | |
| 54 <option value="dmelanogaster_gene_ensembl">Drosophila melanogaster</option> | |
| 55 <option value="etelfairi_gene_ensembl">Echinops telfairi</option> | |
| 56 <option value="ecaballus_gene_ensembl">Equus caballus</option> | |
| 57 <option value="eeuropaeus_gene_ensembl">Erinaceus europaeus</option> | |
| 58 <option value="fcatus_gene_ensembl">Felis catus</option> | |
| 59 <option value="gmorhua_gene_ensembl">Gadus morhua</option> | |
| 60 <option value="gaculeatus_gene_ensembl">Gasterosteus aculeatus</option> | |
| 61 <option value="ggorilla_gene_ensembl">Gorilla gorilla</option> | |
| 62 <option value="itridecemlineatus_gene_ensembl">Ictidomys tridecemlineatus</option> | |
| 63 <option value="lchalumnae_gene_ensembl">Latimeria chalumnae</option> | |
| 64 <option value="lafricana_gene_ensembl">Loxodonta africana</option> | |
| 65 <option value="mmulatta_gene_ensembl">Macaca mulatta</option> | |
| 66 <option value="meugenii_gene_ensembl">Macropus eugenii</option> | |
| 67 <option value="mgallopavo_gene_ensembl">Meleagris gallopavo</option> | |
| 68 <option value="mmurinus_gene_ensembl">Microcebus murinus</option> | |
| 69 <option value="mdomestica_gene_ensembl">Monodelphis domestica</option> | |
| 70 <option value="mlucifugus_gene_ensembl">Myotis lucifugus</option> | |
| 71 <option value="nleucogenys_gene_ensembl">Nomascus leucogenys</option> | |
| 72 <option value="oprinceps_gene_ensembl">Ochotona princeps</option> | |
| 73 <option value="oniloticus_gene_ensembl">Oreochromis niloticus</option> | |
| 74 <option value="oanatinus_gene_ensembl">Ornithorhynchus anatinus</option> | |
| 75 <option value="ocuniculus_gene_ensembl">Oryctolagus cuniculus</option> | |
| 76 <option value="olatipes_gene_ensembl">Oryzias latipes</option> | |
| 77 <option value="ogarnettii_gene_ensembl">Otolemur garnettii</option> | |
| 78 <option value="ptroglodytes_gene_ensembl">Pan troglodytes</option> | |
| 79 <option value="psinensis_gene_ensembl">Pelodiscus sinensis</option> | |
| 80 <option value="pmarinus_gene_ensembl">Petromyzon marinus</option> | |
| 81 <option value="pabelii_gene_ensembl">Pongo abelii</option> | |
| 82 <option value="pcapensis_gene_ensembl">Procavia capensis</option> | |
| 83 <option value="pvampyrus_gene_ensembl">Pteropus vampyrus</option> | |
| 84 <option value="scerevisiae_gene_ensembl">Saccharomyces cerevisiae</option> | |
| 85 <option value="sharrisii_gene_ensembl">Sarcophilus harrisii</option> | |
| 86 <option value="saraneus_gene_ensembl">Sorex araneus</option> | |
| 87 <option value="sscrofa_gene_ensembl">Sus scrofa</option> | |
| 88 <option value="tguttata_gene_ensembl">Taeniopygia guttata</option> | |
| 89 <option value="trubripes_gene_ensembl">Takifugu rubripes</option> | |
| 90 <option value="tsyrichta_gene_ensembl">Tarsius syrichta</option> | |
| 91 <option value="tnigroviridis_gene_ensembl">Tetraodon nigroviridis</option> | |
| 92 <option value="tbelangeri_gene_ensembl">Tupaia belangeri</option> | |
| 93 <option value="ttruncatus_gene_ensembl">Tursiops truncatus</option> | |
| 94 <option value="vpacos_gene_ensembl">Vicugna pacos</option> | |
| 95 <option value="xtropicalis_gene_ensembl">Xenopus tropicalis</option> | |
| 96 </param> | |
| 97 <param name="effects_filter" type="select" optional="true" multiple="true" label="Filter SnpEffect" help="Report coding changes for selected effects"> | |
| 98 <!-- http://snpeff.sourceforge.net/faq.html#What_effects_are_predicted? --> | |
| 99 <option value="FRAME_SHIFT">FRAME_SHIFT</option> | |
| 100 <option value="NON_SYNONYMOUS_CODING">NON_SYNONYMOUS_CODING</option> | |
| 101 <option value="SPLICE_SITE_ACCEPTOR">SPLICE_SITE_ACCEPTOR</option> | |
| 102 <option value="SPLICE_SITE_DONOR">SPLICE_SITE_DONOR</option> | |
| 103 <option value="START_LOST">START_LOST</option> | |
| 104 <option value="EXON_DELETED">EXON_DELETED</option> | |
| 105 <option value="STOP_GAINED">STOP_GAINED</option> | |
| 106 <option value="STOP_LOST">STOP_LOST</option> | |
| 107 <option value="RARE_AMINO_ACID">RARE_AMINO_ACID</option> | |
| 108 <option value="CODON_CHANGE">CODON_CHANGE</option> | |
| 109 <option value="CODON_INSERTION">CODON_INSERTION</option> | |
| 110 <option value="CODON_CHANGE_PLUS_CODON_INSERTION">CODON_CHANGE_PLUS_CODON_INSERTION</option> | |
| 111 <option value="CODON_DELETION">CODON_DELETION</option> | |
| 112 <option value="CODON_CHANGE_PLUS_CODON_DELETION">CODON_CHANGE_PLUS_CODON_DELETION</option> | |
| 113 <option value="UTR_5_DELETED">UTR_5_DELETED</option> | |
| 114 <option value="UTR_3_DELETED">UTR_3_DELETED</option> | |
| 115 <option value="SYNONYMOUS_START">SYNONYMOUS_START</option> | |
| 116 <option value="NON_SYNONYMOUS_START">NON_SYNONYMOUS_START</option> | |
| 117 <option value="START_GAINED">START_GAINED</option> | |
| 118 <option value="SYNONYMOUS_CODING">SYNONYMOUS_CODING</option> | |
| 119 <option value="SYNONYMOUS_STOP">SYNONYMOUS_STOP</option> | |
| 120 <option value="UTR_5_PRIME">UTR_5_PRIME</option> | |
| 121 <option value="UTR_3_PRIME">UTR_3_PRIME</option> | |
| 122 <option value="REGULATION">REGULATION</option> | |
| 123 <option value="UPSTREAM">UPSTREAM</option> | |
| 124 <option value="DOWNSTREAM">DOWNSTREAM</option> | |
| 125 <option value="GENE">GENE</option> | |
| 126 <option value="TRANSCRIPT">TRANSCRIPT</option> | |
| 127 <option value="EXON">EXON</option> | |
| 128 <option value="INTRON_CONSERVED">INTRON_CONSERVED</option> | |
| 129 <option value="INTRON">INTRON</option> | |
| 130 <option value="INTRAGENIC">INTRAGENIC</option> | |
| 131 <option value="INTERGENIC">INTERGENIC</option> | |
| 132 <option value="INTERGENIC_CONSERVED">INTERGENIC_CONSERVED</option> | |
| 133 <option value="NONE">NONE</option> | |
| 134 <option value="CHROMOSOME">CHROMOSOME</option> | |
| 135 <option value="CUSTOM">CUSTOM</option> | |
| 136 <option value="CDS">CDS</option> | |
| 137 </param> | |
| 138 <param name="all_effects" type="boolean" truevalue="--all_effects" falsevalue="" checked="false" label="Report the variant coding for each Ensembl Transcript at the variant position" help="Default is to report only the first Transcript that has a cDNA change"/> | |
| 139 <param name="with_ccds" type="boolean" truevalue="--with_ccds" falsevalue="" checked="false" label="Report the variant coding only for Ensembl Transcripts with a CCDS ID" help=""/> | |
|
5
85b933b7d231
Make the reporting of the SnpEff Amino_Acid_change field an option
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
|
140 <param name="snpeff_aa_change" type="boolean" truevalue="--snpeff_aa_change" falsevalue="" checked="false" label="Report the Amino_Acid_change from SnpEff" help="Otherwise, report the first changed Animo Acid as: AposA (ref_AA pos_from_Nterminus alt_AA)"/> |
| 0 | 141 <param name="polya" type="integer" value="5" optional="true" label="Ignore variants that are part of a Poly-A of at least this length" help="Leave blank to turn off poly A filtering"> |
| 142 <validator type="in_range" message="poly A between 2 and 100 bases" min="2" max="100"/> | |
| 143 </param> | |
| 144 <param name="report_format" type="select" force_select="true" multiple="true" display="checkboxes" label="Report formats" help=""> | |
| 145 <option value="html" selected="true">Detailed HTML report</option> | |
| 146 <option value="tsv" selected="true">TAB-delimited report</option> | |
| 147 <option value="detailed">Detailed Text report</option> | |
| 148 </param> | |
| 149 </inputs> | |
| 150 <outputs> | |
| 151 <data format="html" name="html_report" label="Variant Detection Report (html) on ${on_string}"> | |
| 152 <filter>'html' in report_format</filter> | |
| 153 </data> | |
| 154 <data format="tabular" name="tsv_report" label="Variant Detection Report (tsv) on ${on_string}"> | |
| 155 <filter>'tsv' in report_format</filter> | |
| 156 </data> | |
| 157 <data format="text" name="text_report" label="Variant Detection Report (text) on ${on_string}"> | |
| 158 <filter>'detailed' in report_format</filter> | |
| 159 </data> | |
| 160 </outputs> | |
| 161 <tests> | |
| 162 <test> | |
| 163 <param name="snp_effect_vcf" ftype="vcf" value="snpeff.vcf"/> | |
| 164 <param name="ensembl_host" value="feb2012"/> | |
| 165 <param name="ensembl_dataset" value="hsapiens_gene_ensembl"/> | |
| 166 <param name="effects_filter" value="FRAME_SHIFT"/> | |
| 167 <param name="effects_filter" value="FRAME_SHIFT"/> | |
| 168 <param name="all_effects" value="false"/> | |
| 169 <param name="with_ccds" value="true"/> | |
| 170 <param name="polya" value="5"/> | |
| 171 <param name="report_format" value="tsv"/> | |
| 172 <output name="tsv_report"> | |
| 173 <assert_contents> | |
| 174 <has_text text="46871931" /> | |
| 175 <has_text text="109461327" /> | |
| 176 <not_has_text text="54291558" /> | |
| 177 </assert_contents> | |
| 178 </output> | |
| 179 </test> | |
| 180 </tests> | |
| 181 <help> | |
| 182 **SnpEff Variant Detection Ensembl Report** | |
| 183 | |
| 184 Generates the variant sequence and its translation for the variations reported by SnpEffect_. | |
| 185 The SnpEffect_ output must be in the VCF format, and must include Ensembl Transcript IDs. SnpSift_ can be used to filter the SnpEffect_ VCF output. | |
| 186 | |
| 187 The sequences are retrieved from a biomart server using the xml query interface with the Ensembl Transcript ID as the query key. | |
| 188 | |
| 189 .. _SnpEffect: http://snpeff.sourceforge.net/ | |
| 190 .. _SnpSift: http://snpeff.sourceforge.net/SnpSift.html | |
| 191 | |
| 192 </help> | |
| 193 </tool> |