Mercurial > repos > jjohnson > ensembl_cdna_translate
comparison ensembl_cdna_translate.xml @ 0:a8218b11216f draft
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| author | jjohnson |
|---|---|
| date | Wed, 29 Nov 2017 15:55:59 -0500 |
| parents | |
| children | b7f2f5e3390c |
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| -1:000000000000 | 0:a8218b11216f |
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| 1 <tool id="ensembl_cdna_translate" name="Ensembl cDNA Translations" version="0.1.0"> | |
| 2 <description>using Ensembl REST API</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.4.10">requests-cache</requirement> | |
| 5 <requirement type="package" version="1.62">biopython</requirement> | |
| 6 </requirements> | |
| 7 <stdio> | |
| 8 <exit_code range="1:" /> | |
| 9 </stdio> | |
| 10 <command><![CDATA[ | |
| 11 #if $input: | |
| 12 cat '$input' | |
| 13 #else | |
| 14 python '$__tool_directory__/ensembl_cdna_translate.py' | |
| 15 #if $species: | |
| 16 --species '$species' | |
| 17 #end if | |
| 18 $transcript_raw | |
| 19 #if $biotypes: | |
| 20 --biotypes '$biotypes' | |
| 21 #end if | |
| 22 #if str($output_choice).find('transcript_bed') >= 0: | |
| 23 --transcripts | |
| 24 #if str($output_choice).find('translation') >= 0: | |
| 25 '-' | tee '$transcript_bed' | |
| 26 #else | |
| 27 '$transcript_bed' | |
| 28 #end if | |
| 29 #elif str($output_choice).find('translation') >= 0: | |
| 30 --transcripts '-' | |
| 31 #end if | |
| 32 #end if | |
| 33 #if str($output_choice).find('translation') >= 0: | |
| 34 | python '$__tool_directory__/ensembl_cdna_translate.py' -i '-' | |
| 35 #if $input and str($output_choice).find('transcript_bed') >= 0: | |
| 36 --transcripts '$transcript_bed | |
| 37 #end if | |
| 38 #if str($output_choice).find('translation_bed') >= 0: | |
| 39 --bed '$translation_bed' | |
| 40 #end if | |
| 41 #if str($output_choice).find('translation_fasta') >= 0: | |
| 42 --fasta '$translation_fasta' | |
| 43 #end if | |
| 44 #if $enzyme: | |
| 45 --enzyme '$enzyme' | |
| 46 #end if | |
| 47 #end if | |
| 48 | |
| 49 ]]></command> | |
| 50 <inputs> | |
| 51 <param name="species" type="text" value="" label="Ensembl species" > | |
| 52 <help> | |
| 53 </help> | |
| 54 <option value="homo_sapiens">homo_sapiens (Human) taxon_id: 9606</option> | |
| 55 <option value="mus_musculus">mus_musculus (Mouse) taxon_id: 10090</option> | |
| 56 <option value="ailuropoda_melanoleuca">ailuropoda_melanoleuca (Panda) taxon_id: 9646</option> | |
| 57 <option value="anas_platyrhynchos">anas_platyrhynchos (Duck) taxon_id: 8839</option> | |
| 58 <option value="anolis_carolinensis">anolis_carolinensis (Anole lizard) taxon_id: 28377</option> | |
| 59 <option value="astyanax_mexicanus">astyanax_mexicanus (Cave fish) taxon_id: 7994</option> | |
| 60 <option value="bos_taurus">bos_taurus (Cow) taxon_id: 9913</option> | |
| 61 <option value="caenorhabditis_elegans">caenorhabditis_elegans (Caenorhabditis elegans) taxon_id: 6239</option> | |
| 62 <option value="callithrix_jacchus">callithrix_jacchus (Marmoset) taxon_id: 9483</option> | |
| 63 <option value="canis_familiaris">canis_familiaris (Dog) taxon_id: 9615</option> | |
| 64 <option value="carlito_syrichta">carlito_syrichta (Tarsier) taxon_id: 1868482</option> | |
| 65 <option value="cavia_aperea">cavia_aperea (Brazilian guinea pig) taxon_id: 37548</option> | |
| 66 <option value="cavia_porcellus">cavia_porcellus (Guinea Pig) taxon_id: 10141</option> | |
| 67 <option value="chinchilla_lanigera">chinchilla_lanigera (Long-tailed chinchilla) taxon_id: 34839</option> | |
| 68 <option value="chlorocebus_sabaeus">chlorocebus_sabaeus (Vervet-AGM) taxon_id: 60711</option> | |
| 69 <option value="choloepus_hoffmanni">choloepus_hoffmanni (Sloth) taxon_id: 9358</option> | |
| 70 <option value="ciona_intestinalis">ciona_intestinalis (C.intestinalis) taxon_id: 7719</option> | |
| 71 <option value="ciona_savignyi">ciona_savignyi (C.savignyi) taxon_id: 51511</option> | |
| 72 <option value="cricetulus_griseus_chok1gshd">cricetulus_griseus_chok1gshd (Chinese hamster CHOK1GS) taxon_id: 10029</option> | |
| 73 <option value="cricetulus_griseus_crigri">cricetulus_griseus_crigri (Chinese hamster CriGri) taxon_id: 10029</option> | |
| 74 <option value="danio_rerio">danio_rerio (Zebrafish) taxon_id: 7955</option> | |
| 75 <option value="dasypus_novemcinctus">dasypus_novemcinctus (Armadillo) taxon_id: 9361</option> | |
| 76 <option value="dipodomys_ordii">dipodomys_ordii (Kangaroo rat) taxon_id: 10020</option> | |
| 77 <option value="drosophila_melanogaster">drosophila_melanogaster (Fruitfly) taxon_id: 7227</option> | |
| 78 <option value="echinops_telfairi">echinops_telfairi (Lesser hedgehog tenrec) taxon_id: 9371</option> | |
| 79 <option value="equus_caballus">equus_caballus (Horse) taxon_id: 9796</option> | |
| 80 <option value="erinaceus_europaeus">erinaceus_europaeus (Hedgehog) taxon_id: 9365</option> | |
| 81 <option value="felis_catus">felis_catus (Cat) taxon_id: 9685</option> | |
| 82 <option value="ficedula_albicollis">ficedula_albicollis (Flycatcher) taxon_id: 59894</option> | |
| 83 <option value="fukomys_damarensis">fukomys_damarensis (Damara mole rat) taxon_id: 885580</option> | |
| 84 <option value="gadus_morhua">gadus_morhua (Cod) taxon_id: 8049</option> | |
| 85 <option value="gallus_gallus">gallus_gallus (Chicken) taxon_id: 9031</option> | |
| 86 <option value="gasterosteus_aculeatus">gasterosteus_aculeatus (Stickleback) taxon_id: 69293</option> | |
| 87 <option value="gorilla_gorilla">gorilla_gorilla (Gorilla) taxon_id: 9595</option> | |
| 88 <option value="heterocephalus_glaber_female">heterocephalus_glaber_female (Naked mole-rat female) taxon_id: 10181</option> | |
| 89 <option value="heterocephalus_glaber_male">heterocephalus_glaber_male (Naked mole-rat male) taxon_id: 10181</option> | |
| 90 <option value="ictidomys_tridecemlineatus">ictidomys_tridecemlineatus (Squirrel) taxon_id: 43179</option> | |
| 91 <option value="jaculus_jaculus">jaculus_jaculus (Lesser Egyptian jerboa) taxon_id: 51337</option> | |
| 92 <option value="latimeria_chalumnae">latimeria_chalumnae (Coelacanth) taxon_id: 7897</option> | |
| 93 <option value="lepisosteus_oculatus">lepisosteus_oculatus (Spotted gar) taxon_id: 7918</option> | |
| 94 <option value="loxodonta_africana">loxodonta_africana (Elephant) taxon_id: 9785</option> | |
| 95 <option value="macaca_mulatta">macaca_mulatta (Macaque) taxon_id: 9544</option> | |
| 96 <option value="meleagris_gallopavo">meleagris_gallopavo (Turkey) taxon_id: 9103</option> | |
| 97 <option value="mesocricetus_auratus">mesocricetus_auratus (Golden Hamster) taxon_id: 10036</option> | |
| 98 <option value="microcebus_murinus">microcebus_murinus (Mouse Lemur) taxon_id: 30608</option> | |
| 99 <option value="microtus_ochrogaster">microtus_ochrogaster (Prairie vole) taxon_id: 79684</option> | |
| 100 <option value="monodelphis_domestica">monodelphis_domestica (Opossum) taxon_id: 13616</option> | |
| 101 <option value="mus_caroli">mus_caroli (Ryukyu mouse) taxon_id: 10089</option> | |
| 102 <option value="mus_musculus_129s1svimj">mus_musculus_129s1svimj (Mouse 129S1/SvImJ) taxon_id: 10090</option> | |
| 103 <option value="mus_musculus_aj">mus_musculus_aj (Mouse A/J) taxon_id: 10090</option> | |
| 104 <option value="mus_musculus_akrj">mus_musculus_akrj (Mouse AKR/J) taxon_id: 10090</option> | |
| 105 <option value="mus_musculus_balbcj">mus_musculus_balbcj (Mouse BALB/cJ) taxon_id: 10090</option> | |
| 106 <option value="mus_musculus_c3hhej">mus_musculus_c3hhej (Mouse C3H/HeJ) taxon_id: 10090</option> | |
| 107 <option value="mus_musculus_c57bl6nj">mus_musculus_c57bl6nj (Mouse C57BL/6NJ) taxon_id: 10090</option> | |
| 108 <option value="mus_musculus_casteij">mus_musculus_casteij (Mouse CAST/EiJ) taxon_id: 10091</option> | |
| 109 <option value="mus_musculus_cbaj">mus_musculus_cbaj (Mouse CBA/J) taxon_id: 10090</option> | |
| 110 <option value="mus_musculus_dba2j">mus_musculus_dba2j (Mouse DBA/2J) taxon_id: 10090</option> | |
| 111 <option value="mus_musculus_fvbnj">mus_musculus_fvbnj (Mouse FVB/NJ) taxon_id: 10090</option> | |
| 112 <option value="mus_musculus_lpj">mus_musculus_lpj (Mouse LP/J) taxon_id: 10090</option> | |
| 113 <option value="mus_musculus_nodshiltj">mus_musculus_nodshiltj (Mouse NOD/ShiLtJ) taxon_id: 10090</option> | |
| 114 <option value="mus_musculus_nzohlltj">mus_musculus_nzohlltj (Mouse NZO/HlLtJ) taxon_id: 10090</option> | |
| 115 <option value="mus_musculus_pwkphj">mus_musculus_pwkphj (Mouse PWK/PhJ) taxon_id: 39442</option> | |
| 116 <option value="mus_musculus_wsbeij">mus_musculus_wsbeij (Mouse WSB/EiJ) taxon_id: 10092</option> | |
| 117 <option value="mus_pahari">mus_pahari (Shrew mouse) taxon_id: 10093</option> | |
| 118 <option value="mus_spretus_spreteij">mus_spretus_spreteij (Algerian mouse) taxon_id: 10096</option> | |
| 119 <option value="mustela_putorius_furo">mustela_putorius_furo (Ferret) taxon_id: 9669</option> | |
| 120 <option value="myotis_lucifugus">myotis_lucifugus (Microbat) taxon_id: 59463</option> | |
| 121 <option value="nannospalax_galili">nannospalax_galili (Upper Galilee mountains blind mole rat) taxon_id: 1026970</option> | |
| 122 <option value="nomascus_leucogenys">nomascus_leucogenys (Gibbon) taxon_id: 61853</option> | |
| 123 <option value="notamacropus_eugenii">notamacropus_eugenii (Wallaby) taxon_id: 9315</option> | |
| 124 <option value="ochotona_princeps">ochotona_princeps (Pika) taxon_id: 9978</option> | |
| 125 <option value="octodon_degus">octodon_degus (Degu) taxon_id: 10160</option> | |
| 126 <option value="oreochromis_niloticus">oreochromis_niloticus (Tilapia) taxon_id: 8128</option> | |
| 127 <option value="ornithorhynchus_anatinus">ornithorhynchus_anatinus (Platypus) taxon_id: 9258</option> | |
| 128 <option value="oryctolagus_cuniculus">oryctolagus_cuniculus (Rabbit) taxon_id: 9986</option> | |
| 129 <option value="oryzias_latipes">oryzias_latipes (Medaka) taxon_id: 8090</option> | |
| 130 <option value="otolemur_garnettii">otolemur_garnettii (Bushbaby) taxon_id: 30611</option> | |
| 131 <option value="ovis_aries">ovis_aries (Sheep) taxon_id: 9940</option> | |
| 132 <option value="pan_troglodytes">pan_troglodytes (Chimpanzee) taxon_id: 9598</option> | |
| 133 <option value="papio_anubis">papio_anubis (Olive baboon) taxon_id: 9555</option> | |
| 134 <option value="pelodiscus_sinensis">pelodiscus_sinensis (Chinese softshell turtle) taxon_id: 13735</option> | |
| 135 <option value="peromyscus_maniculatus_bairdii">peromyscus_maniculatus_bairdii (Northern American deer mouse) taxon_id: 230844</option> | |
| 136 <option value="petromyzon_marinus">petromyzon_marinus (Lamprey) taxon_id: 7757</option> | |
| 137 <option value="poecilia_formosa">poecilia_formosa (Amazon molly) taxon_id: 48698</option> | |
| 138 <option value="pongo_abelii">pongo_abelii (Orangutan) taxon_id: 9601</option> | |
| 139 <option value="procavia_capensis">procavia_capensis (Hyrax) taxon_id: 9813</option> | |
| 140 <option value="pteropus_vampyrus">pteropus_vampyrus (Megabat) taxon_id: 132908</option> | |
| 141 <option value="rattus_norvegicus">rattus_norvegicus (Rat) taxon_id: 10116</option> | |
| 142 <option value="saccharomyces_cerevisiae">saccharomyces_cerevisiae (Saccharomyces cerevisiae) taxon_id: 4932</option> | |
| 143 <option value="sarcophilus_harrisii">sarcophilus_harrisii (Tasmanian devil) taxon_id: 9305</option> | |
| 144 <option value="sorex_araneus">sorex_araneus (Shrew) taxon_id: 42254</option> | |
| 145 <option value="sus_scrofa">sus_scrofa (Pig) taxon_id: 9823</option> | |
| 146 <option value="taeniopygia_guttata">taeniopygia_guttata (Zebra Finch) taxon_id: 59729</option> | |
| 147 <option value="takifugu_rubripes">takifugu_rubripes (Fugu) taxon_id: 31033</option> | |
| 148 <option value="tetraodon_nigroviridis">tetraodon_nigroviridis (Tetraodon) taxon_id: 99883</option> | |
| 149 <option value="tupaia_belangeri">tupaia_belangeri (Tree Shrew) taxon_id: 37347</option> | |
| 150 <option value="tursiops_truncatus">tursiops_truncatus (Dolphin) taxon_id: 9739</option> | |
| 151 <option value="vicugna_pacos">vicugna_pacos (Alpaca) taxon_id: 30538</option> | |
| 152 <option value="xenopus_tropicalis">xenopus_tropicalis (Xenopus) taxon_id: 8364</option> | |
| 153 <option value="xiphophorus_maculatus">xiphophorus_maculatus (Platyfish) taxon_id: 8083</option> | |
| 154 | |
| 155 </param> | |
| 156 <param name="biotypes" type="text" value="" optional="true" label="Restrict to these biotypes" > | |
| 157 <help><![CDATA[ | |
| 158 Example biotypes: | |
| 159 protein_coding, non_coding, pseudogene, nonsense_mediated_decay, non_stop_decay, | |
| 160 translated_processed_pseudogene, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, transcribed_unprocessed_pseudogene, | |
| 161 polymorphic_pseudogene, processed_pseudogene, unprocessed_pseudogene, unitary_pseudogene, processed_transcript, | |
| 162 retained_intron, ccds_gene, sense_overlapping, sense_intronic, cdna_update, antisense, | |
| 163 LRG_gene, IG_C_gene, IG_D_gene, IG_J_gene, IG_LV_gene IG_V_gene, TR_C_gene, TR_D_gene, TR_J_gene, TR_V_gene, | |
| 164 IG_pseudogene, IG_C_pseudogene, IG_D_pseudogene, IG_J_pseudogene, IG_V_pseudogene, TR_J_pseudogene, TR_V_pseudogene, TEC, | |
| 165 ribozyme, RNase_P_RNA, guide_RNA, macro_lncRNA, bidirectional_promoter_lncRNA, 3prime_overlapping_ncRNA, antisense_RNA, vaultRNA, Y_RNA, SRP_RNA, RNase_MRP_RNA, IG_C_pseudogene, lncRNA, lincRNA, miRNA, snRNA, sRNA, telomerase_RNA, Mt_tRNA, Mt_rRNA, scaRNA, misc_RNA, rRNA, tRNA, scRNA, snoRNA, other | |
| 166 ]]></help> | |
| 167 </param> | |
| 168 <param name="input" type="data" format="bed" optional="true" label="A BED file with 12 columns, thickStart and thickEnd define protein coding region"/> | |
| 169 <param name="translate_all" type="boolean" truevalue="--all" falsevalue="" checked="false" | |
| 170 label="Report all translations (Default is non reference protein sequences)"/> | |
| 171 <param name="transcript_raw" type="boolean" truevalue="--raw" falsevalue="" checked="true" | |
| 172 label="Keep extra columns from ensembl BED"/> | |
| 173 <param name="output_choice" type="select" multiple="true" display="checkboxes" label="Outputs"> | |
| 174 <option value="transcript_bed">transcripts.bed</option> | |
| 175 <option value="translation_bed">translation.bed</option> | |
| 176 <option value="translation_fasta">translation.fasta</option> | |
| 177 </param> | |
| 178 <param name="min_length" type="integer" value="7" min="1" label="Minimum length of protein translation to report"/> | |
| 179 <param name="enzyme" type="select" optional="true" label="Digest enzyme" | |
| 180 help="Remove frags that are in a reference protein"> | |
| 181 <option value="trypsin">trypsin: ([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=P))</option> | |
| 182 </param> | |
| 183 </inputs> | |
| 184 <outputs> | |
| 185 <data name="transcript_bed" format="bed" label="Ensembl $species transcripts.bed"> | |
| 186 <filter>'transcript_bed' in output_choice</filter> | |
| 187 </data> | |
| 188 <data name="translation_bed" format="bed" label="Ensembl $species translation.bed"> | |
| 189 <filter>'translation_bed' in output_choice</filter> | |
| 190 </data> | |
| 191 <data name="translation_fasta" format="fasta" label="Ensembl $species translation.fasta"> | |
| 192 <filter>'translation_fasta' in output_choice</filter> | |
| 193 </data> | |
| 194 </outputs> | |
| 195 <tests> | |
| 196 <test> | |
| 197 <param name="species" value="human"/> | |
| 198 <param name="input" value="human_transcripts.bed" ftype="bed"/> | |
| 199 <param name="output_choice" value="translation_bed,translation_fasta"/> | |
| 200 <output name="translation_bed"> | |
| 201 <assert_contents> | |
| 202 <has_text text="ENST00000641515" /> | |
| 203 </assert_contents> | |
| 204 </output> | |
| 205 <output name="translation_fasta"> | |
| 206 <assert_contents> | |
| 207 <has_text text=">ENST00000641515" /> | |
| 208 </assert_contents> | |
| 209 </output> | |
| 210 </test> | |
| 211 </tests> | |
| 212 <help><![CDATA[ | |
| 213 usage: ensembl_cdna_translate.py [-h] [-s SPECIES] [-i INPUT] [-t TRANSCRIPTS] | |
| 214 [-r] [-f FASTA] [-b BED] [-m MIN_LENGTH] [-a] | |
| 215 [-v] [-d] | |
| 216 | |
| 217 Retrieve Ensembl cDNAs and three frame translate | |
| 218 | |
| 219 optional arguments: | |
| 220 -h, --help show this help message and exit | |
| 221 -s SPECIES, --species SPECIES | |
| 222 Ensembl Species to retrieve | |
| 223 -i INPUT, --input INPUT | |
| 224 Use this bed instead of retrieving cDNA from ensembl | |
| 225 (-) for stdin | |
| 226 -t TRANSCRIPTS, --transcripts TRANSCRIPTS | |
| 227 Path to output cDNA transcripts.bed (-) for stdout | |
| 228 -r, --raw Report transcript exacty as returned from Ensembl | |
| 229 -f FASTA, --fasta FASTA | |
| 230 Path to output translations.fasta | |
| 231 -b BED, --bed BED Path to output translations.bed | |
| 232 -m MIN_LENGTH, --min_length MIN_LENGTH | |
| 233 Minimum length of protein translation to report | |
| 234 -a, --all Report all translations (Default is non reference | |
| 235 protein sequences) | |
| 236 -v, --verbose Verbose | |
| 237 -d, --debug Debug | |
| 238 | |
| 239 Esmebl REST API returns a 20 BED format with these additional columns:: | |
| 240 | |
| 241 second_name, cds_start_status, cds_end_status, exon_frames, type, gene_name, second_gene_name, gene_type | |
| 242 | |
| 243 ]]></help> | |
| 244 <citations> | |
| 245 <citation type="doi">10.1093/bioinformatics/btu613</citation> | |
| 246 <citation type="doi">10.1093/nar/gku1010</citation> | |
| 247 </citations> | |
| 248 </tool> |