Mercurial > repos > jjohnson > ensembl_cdna_translate
diff ensembl_cdna_translate.xml @ 7:d59e3ce10e74 draft
Uploaded
| author | jjohnson |
|---|---|
| date | Wed, 13 Dec 2017 11:15:34 -0500 |
| parents | f8e0e5e237a5 |
| children | 5c92d0be6514 |
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--- a/ensembl_cdna_translate.xml Wed Nov 29 17:46:00 2017 -0500 +++ b/ensembl_cdna_translate.xml Wed Dec 13 11:15:34 2017 -0500 @@ -1,5 +1,8 @@ <tool id="ensembl_cdna_translate" name="Ensembl cDNA Translations" version="0.1.0"> <description>using Ensembl REST API</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> <requirement type="package" version="0.4.10">requests-cache</requirement> <requirement type="package" version="1.62">biopython</requirement> @@ -8,16 +11,19 @@ <exit_code range="1:" /> </stdio> <command><![CDATA[ - #if $input: - cat '$input' + #if $features.feature_src == 'history_bed': + cat '$features.input' #else python '$__tool_directory__/ensembl_cdna_translate.py' #if $species: --species '$species' #end if - $transcript_raw - #if $biotypes: - --biotypes '$biotypes' + $features.transcript_raw + #if $features.biotypes: + --biotypes '$features.biotypes' + #end if + #if $features.regions: + --regions '$features.regions' #end if #if str($output_choice).find('transcript_bed') >= 0: --transcripts @@ -45,6 +51,9 @@ #if str($output_choice).find('translation_fasta') >= 0: --fasta '$translation_fasta' #end if + ###if $features.biotypes: + ## --biotypes '$features.biotypes' + ###end if #end if ]]></command> @@ -52,125 +61,40 @@ <param name="species" type="text" value="" label="Ensembl species" > <help> </help> - <option value="homo_sapiens">homo_sapiens (Human) taxon_id: 9606</option> - <option value="mus_musculus">mus_musculus (Mouse) taxon_id: 10090</option> - <option value="ailuropoda_melanoleuca">ailuropoda_melanoleuca (Panda) taxon_id: 9646</option> - <option value="anas_platyrhynchos">anas_platyrhynchos (Duck) taxon_id: 8839</option> - <option value="anolis_carolinensis">anolis_carolinensis (Anole lizard) taxon_id: 28377</option> - <option value="astyanax_mexicanus">astyanax_mexicanus (Cave fish) taxon_id: 7994</option> - <option value="bos_taurus">bos_taurus (Cow) taxon_id: 9913</option> - <option value="caenorhabditis_elegans">caenorhabditis_elegans (Caenorhabditis elegans) taxon_id: 6239</option> - <option value="callithrix_jacchus">callithrix_jacchus (Marmoset) taxon_id: 9483</option> - <option value="canis_familiaris">canis_familiaris (Dog) taxon_id: 9615</option> - <option value="carlito_syrichta">carlito_syrichta (Tarsier) taxon_id: 1868482</option> - <option value="cavia_aperea">cavia_aperea (Brazilian guinea pig) taxon_id: 37548</option> - <option value="cavia_porcellus">cavia_porcellus (Guinea Pig) taxon_id: 10141</option> - <option value="chinchilla_lanigera">chinchilla_lanigera (Long-tailed chinchilla) taxon_id: 34839</option> - <option value="chlorocebus_sabaeus">chlorocebus_sabaeus (Vervet-AGM) taxon_id: 60711</option> - <option value="choloepus_hoffmanni">choloepus_hoffmanni (Sloth) taxon_id: 9358</option> - <option value="ciona_intestinalis">ciona_intestinalis (C.intestinalis) taxon_id: 7719</option> - <option value="ciona_savignyi">ciona_savignyi (C.savignyi) taxon_id: 51511</option> - <option value="cricetulus_griseus_chok1gshd">cricetulus_griseus_chok1gshd (Chinese hamster CHOK1GS) taxon_id: 10029</option> - <option value="cricetulus_griseus_crigri">cricetulus_griseus_crigri (Chinese hamster CriGri) taxon_id: 10029</option> - <option value="danio_rerio">danio_rerio (Zebrafish) taxon_id: 7955</option> - <option value="dasypus_novemcinctus">dasypus_novemcinctus (Armadillo) taxon_id: 9361</option> - <option value="dipodomys_ordii">dipodomys_ordii (Kangaroo rat) taxon_id: 10020</option> - <option value="drosophila_melanogaster">drosophila_melanogaster (Fruitfly) taxon_id: 7227</option> - <option value="echinops_telfairi">echinops_telfairi (Lesser hedgehog tenrec) taxon_id: 9371</option> - <option value="equus_caballus">equus_caballus (Horse) taxon_id: 9796</option> - <option value="erinaceus_europaeus">erinaceus_europaeus (Hedgehog) taxon_id: 9365</option> - <option value="felis_catus">felis_catus (Cat) taxon_id: 9685</option> - <option value="ficedula_albicollis">ficedula_albicollis (Flycatcher) taxon_id: 59894</option> - <option value="fukomys_damarensis">fukomys_damarensis (Damara mole rat) taxon_id: 885580</option> - <option value="gadus_morhua">gadus_morhua (Cod) taxon_id: 8049</option> - <option value="gallus_gallus">gallus_gallus (Chicken) taxon_id: 9031</option> - <option value="gasterosteus_aculeatus">gasterosteus_aculeatus (Stickleback) taxon_id: 69293</option> - <option value="gorilla_gorilla">gorilla_gorilla (Gorilla) taxon_id: 9595</option> - <option value="heterocephalus_glaber_female">heterocephalus_glaber_female (Naked mole-rat female) taxon_id: 10181</option> - <option value="heterocephalus_glaber_male">heterocephalus_glaber_male (Naked mole-rat male) taxon_id: 10181</option> - <option value="ictidomys_tridecemlineatus">ictidomys_tridecemlineatus (Squirrel) taxon_id: 43179</option> - <option value="jaculus_jaculus">jaculus_jaculus (Lesser Egyptian jerboa) taxon_id: 51337</option> - <option value="latimeria_chalumnae">latimeria_chalumnae (Coelacanth) taxon_id: 7897</option> - <option value="lepisosteus_oculatus">lepisosteus_oculatus (Spotted gar) taxon_id: 7918</option> - <option value="loxodonta_africana">loxodonta_africana (Elephant) taxon_id: 9785</option> - <option value="macaca_mulatta">macaca_mulatta (Macaque) taxon_id: 9544</option> - <option value="meleagris_gallopavo">meleagris_gallopavo (Turkey) taxon_id: 9103</option> - <option value="mesocricetus_auratus">mesocricetus_auratus (Golden Hamster) taxon_id: 10036</option> - <option value="microcebus_murinus">microcebus_murinus (Mouse Lemur) taxon_id: 30608</option> - <option value="microtus_ochrogaster">microtus_ochrogaster (Prairie vole) taxon_id: 79684</option> - <option value="monodelphis_domestica">monodelphis_domestica (Opossum) taxon_id: 13616</option> - <option value="mus_caroli">mus_caroli (Ryukyu mouse) taxon_id: 10089</option> - <option value="mus_musculus_129s1svimj">mus_musculus_129s1svimj (Mouse 129S1/SvImJ) taxon_id: 10090</option> - <option value="mus_musculus_aj">mus_musculus_aj (Mouse A/J) taxon_id: 10090</option> - <option value="mus_musculus_akrj">mus_musculus_akrj (Mouse AKR/J) taxon_id: 10090</option> - <option value="mus_musculus_balbcj">mus_musculus_balbcj (Mouse BALB/cJ) taxon_id: 10090</option> - <option value="mus_musculus_c3hhej">mus_musculus_c3hhej (Mouse C3H/HeJ) taxon_id: 10090</option> - <option value="mus_musculus_c57bl6nj">mus_musculus_c57bl6nj (Mouse C57BL/6NJ) taxon_id: 10090</option> - <option value="mus_musculus_casteij">mus_musculus_casteij (Mouse CAST/EiJ) taxon_id: 10091</option> - <option value="mus_musculus_cbaj">mus_musculus_cbaj (Mouse CBA/J) taxon_id: 10090</option> - <option value="mus_musculus_dba2j">mus_musculus_dba2j (Mouse DBA/2J) taxon_id: 10090</option> - <option value="mus_musculus_fvbnj">mus_musculus_fvbnj (Mouse FVB/NJ) taxon_id: 10090</option> - <option value="mus_musculus_lpj">mus_musculus_lpj (Mouse LP/J) taxon_id: 10090</option> - <option value="mus_musculus_nodshiltj">mus_musculus_nodshiltj (Mouse NOD/ShiLtJ) taxon_id: 10090</option> - <option value="mus_musculus_nzohlltj">mus_musculus_nzohlltj (Mouse NZO/HlLtJ) taxon_id: 10090</option> - <option value="mus_musculus_pwkphj">mus_musculus_pwkphj (Mouse PWK/PhJ) taxon_id: 39442</option> - <option value="mus_musculus_wsbeij">mus_musculus_wsbeij (Mouse WSB/EiJ) taxon_id: 10092</option> - <option value="mus_pahari">mus_pahari (Shrew mouse) taxon_id: 10093</option> - <option value="mus_spretus_spreteij">mus_spretus_spreteij (Algerian mouse) taxon_id: 10096</option> - <option value="mustela_putorius_furo">mustela_putorius_furo (Ferret) taxon_id: 9669</option> - <option value="myotis_lucifugus">myotis_lucifugus (Microbat) taxon_id: 59463</option> - <option value="nannospalax_galili">nannospalax_galili (Upper Galilee mountains blind mole rat) taxon_id: 1026970</option> - <option value="nomascus_leucogenys">nomascus_leucogenys (Gibbon) taxon_id: 61853</option> - <option value="notamacropus_eugenii">notamacropus_eugenii (Wallaby) taxon_id: 9315</option> - <option value="ochotona_princeps">ochotona_princeps (Pika) taxon_id: 9978</option> - <option value="octodon_degus">octodon_degus (Degu) taxon_id: 10160</option> - <option value="oreochromis_niloticus">oreochromis_niloticus (Tilapia) taxon_id: 8128</option> - <option value="ornithorhynchus_anatinus">ornithorhynchus_anatinus (Platypus) taxon_id: 9258</option> - <option value="oryctolagus_cuniculus">oryctolagus_cuniculus (Rabbit) taxon_id: 9986</option> - <option value="oryzias_latipes">oryzias_latipes (Medaka) taxon_id: 8090</option> - <option value="otolemur_garnettii">otolemur_garnettii (Bushbaby) taxon_id: 30611</option> - <option value="ovis_aries">ovis_aries (Sheep) taxon_id: 9940</option> - <option value="pan_troglodytes">pan_troglodytes (Chimpanzee) taxon_id: 9598</option> - <option value="papio_anubis">papio_anubis (Olive baboon) taxon_id: 9555</option> - <option value="pelodiscus_sinensis">pelodiscus_sinensis (Chinese softshell turtle) taxon_id: 13735</option> - <option value="peromyscus_maniculatus_bairdii">peromyscus_maniculatus_bairdii (Northern American deer mouse) taxon_id: 230844</option> - <option value="petromyzon_marinus">petromyzon_marinus (Lamprey) taxon_id: 7757</option> - <option value="poecilia_formosa">poecilia_formosa (Amazon molly) taxon_id: 48698</option> - <option value="pongo_abelii">pongo_abelii (Orangutan) taxon_id: 9601</option> - <option value="procavia_capensis">procavia_capensis (Hyrax) taxon_id: 9813</option> - <option value="pteropus_vampyrus">pteropus_vampyrus (Megabat) taxon_id: 132908</option> - <option value="rattus_norvegicus">rattus_norvegicus (Rat) taxon_id: 10116</option> - <option value="saccharomyces_cerevisiae">saccharomyces_cerevisiae (Saccharomyces cerevisiae) taxon_id: 4932</option> - <option value="sarcophilus_harrisii">sarcophilus_harrisii (Tasmanian devil) taxon_id: 9305</option> - <option value="sorex_araneus">sorex_araneus (Shrew) taxon_id: 42254</option> - <option value="sus_scrofa">sus_scrofa (Pig) taxon_id: 9823</option> - <option value="taeniopygia_guttata">taeniopygia_guttata (Zebra Finch) taxon_id: 59729</option> - <option value="takifugu_rubripes">takifugu_rubripes (Fugu) taxon_id: 31033</option> - <option value="tetraodon_nigroviridis">tetraodon_nigroviridis (Tetraodon) taxon_id: 99883</option> - <option value="tupaia_belangeri">tupaia_belangeri (Tree Shrew) taxon_id: 37347</option> - <option value="tursiops_truncatus">tursiops_truncatus (Dolphin) taxon_id: 9739</option> - <option value="vicugna_pacos">vicugna_pacos (Alpaca) taxon_id: 30538</option> - <option value="xenopus_tropicalis">xenopus_tropicalis (Xenopus) taxon_id: 8364</option> - <option value="xiphophorus_maculatus">xiphophorus_maculatus (Platyfish) taxon_id: 8083</option> + <expand macro="species_options" /> + </param> + <conditional name="features"> + <param name="feature_src" type="select" label="Features to translate"> + <option value="ensembl_rest">Retrieve from Ensembl</option> + <option value="history_bed">Use Ensembl BED file</option> + </param> + <when value="ensembl_rest"> + <param name="transcript_raw" type="boolean" truevalue="--raw" falsevalue="" checked="true" + label="Keep extra columns from ensembl BED"/> + <param name="biotypes" type="text" value="" optional="true" label="Restrict Feature retrieval to these biotypes" > + <expand macro="biotypes_help" /> + </param> + <param name="regions" type="text" value="" optional="true" label="Restrict Feature retrieval to comma-separated list of regions" > + <help>Each region is specifed as: chr or chr:pos or chr:from-to</help> + <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> + </param> + </when> + <when value="history_bed"> + <param name="input" type="data" format="bed" optional="true" label="A BED file with 12 columns" + help="thickStart and thickEnd define protein coding region, blocks define exon regions"/> + <param name="biotypes" type="text" value="" optional="true" label="Restrict Feature translation to these biotypes" > + <expand macro="biotypes_help" /> + </param> + </when> + </conditional> + <!-- + <conditional name="translations"> + </conditional> + --> - </param> - <param name="biotypes" type="text" value="" optional="true" label="Restrict to these biotypes" > - <help><![CDATA[ -Example biotypes: -protein_coding, non_coding, pseudogene, nonsense_mediated_decay, non_stop_decay, -translated_processed_pseudogene, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, transcribed_unprocessed_pseudogene, -polymorphic_pseudogene, processed_pseudogene, unprocessed_pseudogene, unitary_pseudogene, processed_transcript, -retained_intron, ccds_gene, sense_overlapping, sense_intronic, cdna_update, antisense, -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, -IG_pseudogene, IG_C_pseudogene, IG_D_pseudogene, IG_J_pseudogene, IG_V_pseudogene, TR_J_pseudogene, TR_V_pseudogene, TEC, -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 - ]]></help> - </param> - <param name="input" type="data" format="bed" optional="true" label="A BED file with 12 columns, thickStart and thickEnd define protein coding region"/> + <param name="translate_all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="Report all translations (Default is non reference protein sequences)"/> - <param name="transcript_raw" type="boolean" truevalue="--raw" falsevalue="" checked="true" - label="Keep extra columns from ensembl BED"/> <param name="output_choice" type="select" multiple="true" display="checkboxes" label="Outputs"> <option value="transcript_bed">transcripts.bed</option> <option value="translation_bed">translation.bed</option>