Mercurial > repos > dvanzessen > vep_emc

changeset 4:c9f69375e072 draft

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Uploaded
author dvanzessen
date Mon, 15 Jul 2019 09:34:31 -0400
parents 49397129aec0
children 166e1c2b8c35
files data_manager/fetch_vep_cache_data.xml dir_plugins/fetch_vep_cache_data.xml
diffstat 2 files changed, 189 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/fetch_vep_cache_data.xml	Mon Jul 15 05:20:39 2019 -0400
+++ b/data_manager/fetch_vep_cache_data.xml	Mon Jul 15 09:34:31 2019 -0400
@@ -1,6 +1,9 @@
 <tool id="fetch_vep_cache_data" name="VEP Cache" version="0.0.1" tool_type="manage_data">
   <requirements>
     <requirement type="package" version="94.5">ensembl-vep</requirement>
+    <requirement type="package" version="1.642">perl-dbi</requirement>
+    <requirement type="package" version="1.64">perl-archive-zip</requirement>
+    <requirement type="package" version="4.046">perl-dbd-mysql</requirement>
   </requirements>
   <description>fetching</description>
   
@@ -179,4 +182,4 @@
   <help>
   There is no help
   </help>
-</tool>
\ No newline at end of file
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dir_plugins/fetch_vep_cache_data.xml	Mon Jul 15 09:34:31 2019 -0400
@@ -0,0 +1,185 @@
+<tool id="fetch_vep_cache_data" name="VEP Cache" version="0.0.1" tool_type="manage_data">
+  <requirements>
+    <requirement type="package" version="94.5">ensembl-vep</requirement>
+    <requirement type="package" version="1.642">perl-dbi</requirement>
+    <requirement type="package" version="1.64">perl-archive-zip</requirement>
+    <requirement type="package" version="4.046">perl-dbd-mysql</requirement>
+  </requirements>
+  <description>fetching</description>
+  
+  <command detect_errors="exit_code">
+python $__tool_directory__/fetch_vep_cache_data.py 
+--output-file ${ out_file } 
+--output-dir ${ out_file.extra_files_path } 
+--species ${ species }
+--species-type ${ species_type }
+  </command>
+  <inputs>
+    <param name="species" type="select" label="Species">
+      <option value="homo_sapiens37">homo_sapiens (GRCh37)</option>
+      <option value="homo_sapiens38">homo_sapiens (GRCh38)</option>
+      <option value="orycteropus_afer_afer">orycteropus_afer_afer</option>
+      <option value="mus_spretus">mus_spretus</option>
+      <option value="vicugna_pacos">vicugna_pacos</option>
+      <option value="poecilia_formosa">poecilia_formosa</option>
+      <option value="colobus_angolensis_palliatus">colobus_angolensis_palliatus</option>
+      <option value="anolis_carolinensis">anolis_carolinensis</option>
+      <option value="dasypus_novemcinctus">dasypus_novemcinctus</option>
+      <option value="scleropages_formosus">scleropages_formosus</option>
+      <option value="labrus_bergylta">labrus_bergylta</option>
+      <option value="stegastes_partitus">stegastes_partitus</option>
+      <option value="periophthalmus_magnuspinnatus">periophthalmus_magnuspinnatus</option>
+      <option value="rhinopithecus_bieti">rhinopithecus_bieti</option>
+      <option value="saimiri_boliviensis_boliviensis">saimiri_boliviensis_boliviensis</option>
+      <option value="pan_paniscus">pan_paniscus</option>
+      <option value="cavia_aperea">cavia_aperea</option>
+      <option value="melopsittacus_undulatus">melopsittacus_undulatus</option>
+      <option value="haplochromis_burtoni">haplochromis_burtoni</option>
+      <option value="otolemur_garnettii">otolemur_garnettii</option>
+      <option value="ciona_intestinalis">ciona_intestinalis</option>
+      <option value="ciona_savignyi">ciona_savignyi</option>
+      <option value="caenorhabditis_elegans">caenorhabditis_elegans</option>
+      <option value="cebus_capucinus_imitator">cebus_capucinus_imitator</option>
+      <option value="felis_catus">felis_catus</option>
+      <option value="astyanax_mexicanus">astyanax_mexicanus</option>
+      <option value="ictalurus_punctatus">ictalurus_punctatus</option>
+      <option value="gallus_gallus">gallus_gallus</option>
+      <option value="pan_troglodytes">pan_troglodytes</option>
+      <option value="cricetulus_griseus">cricetulus_griseus</option>
+      <option value="pelodiscus_sinensis">pelodiscus_sinensis</option>
+      <option value="anabas_testudineus">anabas_testudineus</option>
+      <option value="amphiprion_ocellaris">amphiprion_ocellaris</option>
+      <option value="gadus_morhua">gadus_morhua</option>
+      <option value="latimeria_chalumnae">latimeria_chalumnae</option>
+      <option value="propithecus_coquereli">propithecus_coquereli</option>
+      <option value="bos_taurus">bos_taurus</option>
+      <option value="macaca_fascicularis">macaca_fascicularis</option>
+      <option value="fukomys_damarensis">fukomys_damarensis</option>
+      <option value="octodon_degus">octodon_degus</option>
+      <option value="canis_lupus_familiaris">canis_lupus_familiaris</option>
+      <option value="tursiops_truncatus">tursiops_truncatus</option>
+      <option value="mandrillus_leucophaeus">mandrillus_leucophaeus</option>
+      <option value="anas_platyrhynchos">anas_platyrhynchos</option>
+      <option value="astatotilapia_calliptera">astatotilapia_calliptera</option>
+      <option value="loxodonta_africana">loxodonta_africana</option>
+      <option value="mustela_putorius_furo">mustela_putorius_furo</option>
+      <option value="ficedula_albicollis">ficedula_albicollis</option>
+      <option value="drosophila_melanogaster">drosophila_melanogaster</option>
+      <option value="takifugu_rubripes">takifugu_rubripes</option>
+      <option value="nomascus_leucogenys">nomascus_leucogenys</option>
+      <option value="capra_hircus">capra_hircus</option>
+      <option value="mesocricetus_auratus">mesocricetus_auratus</option>
+      <option value="rhinopithecus_roxellana">rhinopithecus_roxellana</option>
+      <option value="gorilla_gorilla_gorilla">gorilla_gorilla_gorilla</option>
+      <option value="seriola_dumerili">seriola_dumerili</option>
+      <option value="cavia_porcellus">cavia_porcellus</option>
+      <option value="poecilia_reticulata">poecilia_reticulata</option>
+      <option value="eptatretus_burgeri">eptatretus_burgeri</option>
+      <option value="papio_hamadryas">papio_hamadryas</option>
+      <option value="erinaceus_europaeus">erinaceus_europaeus</option>
+      <option value="equus_caballus">equus_caballus</option>
+      <option value="procavia_capensis">procavia_capensis</option>
+      <option value="oryzias_melastigma">oryzias_melastigma</option>
+      <option value="oryzias_latipes">oryzias_latipes</option>
+      <option value="dipodomys_ordii">dipodomys_ordii</option>
+      <option value="petromyzon_marinus">petromyzon_marinus</option>
+      <option value="panthera_pardus">panthera_pardus</option>
+      <option value="jaculus_jaculus">jaculus_jaculus</option>
+      <option value="echinops_telfairi">echinops_telfairi</option>
+      <option value="chinchilla_lanigera">chinchilla_lanigera</option>
+      <option value="neolamprologus_brichardi">neolamprologus_brichardi</option>
+      <option value="aotus_nancymaae">aotus_nancymaae</option>
+      <option value="macaca_mulatta">macaca_mulatta</option>
+      <option value="kryptolebias_marmoratus">kryptolebias_marmoratus</option>
+      <option value="callithrix_jacchus">callithrix_jacchus</option>
+      <option value="pteropus_vampyrus">pteropus_vampyrus</option>
+      <option value="myotis_lucifugus">myotis_lucifugus</option>
+      <option value="amphilophus_citrinellus">amphilophus_citrinellus</option>
+      <option value="xiphophorus_couchianus">xiphophorus_couchianus</option>
+      <option value="mus_musculus">mus_musculus</option>
+      <option value="mus_musculus_castaneus">mus_musculus_castaneus</option>
+      <option value="microcebus_murinus">microcebus_murinus</option>
+      <option value="mus_musculus_musculus">mus_musculus_musculus</option>
+      <option value="mus_musculus_domesticus">mus_musculus_domesticus</option>
+      <option value="fundulus_heteroclitus">fundulus_heteroclitus</option>
+      <option value="heterocephalus_glaber">heterocephalus_glaber</option>
+      <option value="peromyscus_maniculatus_bairdii">peromyscus_maniculatus_bairdii</option>
+      <option value="esox_lucius">esox_lucius</option>
+      <option value="mola_mola">mola_mola</option>
+      <option value="papio_anubis">papio_anubis</option>
+      <option value="monodelphis_domestica">monodelphis_domestica</option>
+      <option value="amphiprion_percula">amphiprion_percula</option>
+      <option value="pongo_abelii">pongo_abelii</option>
+      <option value="chrysemys_picta_bellii">chrysemys_picta_bellii</option>
+      <option value="ailuropoda_melanoleuca">ailuropoda_melanoleuca</option>
+      <option value="paramormyrops_kingsleyae">paramormyrops_kingsleyae</option>
+      <option value="sus_scrofa">sus_scrofa</option>
+      <option value="sus_scrofa_map">sus_scrofa_map</option>
+      <option value="macaca_nemestrina">macaca_nemestrina</option>
+      <option value="ochotona_princeps">ochotona_princeps</option>
+      <option value="xiphophorus_maculatus">xiphophorus_maculatus</option>
+      <option value="ornithorhynchus_anatinus">ornithorhynchus_anatinus</option>
+      <option value="microtus_ochrogaster">microtus_ochrogaster</option>
+      <option value="pundamilia_nyererei">pundamilia_nyererei</option>
+      <option value="oryctolagus_cuniculus">oryctolagus_cuniculus</option>
+      <option value="rattus_norvegicus">rattus_norvegicus</option>
+      <option value="pygocentrus_nattereri">pygocentrus_nattereri</option>
+      <option value="ceratotherium_simum_simum">ceratotherium_simum_simum</option>
+      <option value="mus_caroli">mus_caroli</option>
+      <option value="saccharomyces_cerevisiae">saccharomyces_cerevisiae</option>
+      <option value="poecilia_latipinna">poecilia_latipinna</option>
+      <option value="ovis_aries">ovis_aries</option>
+      <option value="cyprinodon_variegatus">cyprinodon_variegatus</option>
+      <option value="poecilia_mexicana">poecilia_mexicana</option>
+      <option value="sorex_araneus">sorex_araneus</option>
+      <option value="mus_pahari">mus_pahari</option>
+      <option value="choloepus_hoffmanni">choloepus_hoffmanni</option>
+      <option value="cercocebus_atys">cercocebus_atys</option>
+      <option value="physter_macrocephalus">physter_macrocephalus</option>
+      <option value="acanthochromis_polyacanthus">acanthochromis_polyacanthus</option>
+      <option value="lepisosteus_oculatus">lepisosteus_oculatus</option>
+      <option value="ictidomys_tridecemlineatus">ictidomys_tridecemlineatus</option>
+      <option value="gasterosteus_aculeatus">gasterosteus_aculeatus</option>
+      <option value="monopterus_albus">monopterus_albus</option>
+      <option value="carlito_syrichta">carlito_syrichta</option>
+      <option value="sarcophilus_harrisii">sarcophilus_harrisii</option>
+      <option value="tetraodon_nigroviridis">tetraodon_nigroviridis</option>
+      <option value="panthera_tigris_altaica">panthera_tigris_altaica</option>
+      <option value="hippocampus_comes">hippocampus_comes</option>
+      <option value="oreochromis_niloticus">oreochromis_niloticus</option>
+      <option value="cynoglossus_semilaevis">cynoglossus_semilaevis</option>
+      <option value="tupaia_belangeri">tupaia_belangeri</option>
+      <option value="scophthalmus_maximus">scophthalmus_maximus</option>
+      <option value="meleagris_gallopavo">meleagris_gallopavo</option>
+      <option value="nannospalax_galili">nannospalax_galili</option>
+      <option value="chlorocebus_sabaeus">chlorocebus_sabaeus</option>
+      <option value="notamacropus_eugenii">notamacropus_eugenii</option>
+      <option value="gambusia_affinis">gambusia_affinis</option>
+      <option value="xenopus_tropicalis">xenopus_tropicalis</option>
+      <option value="seriola_lalandi_dorsalis">seriola_lalandi_dorsalis</option>
+      <option value="taeniopygia_guttata">taeniopygia_guttata</option>
+      <option value="maylandia_zebra">maylandia_zebra</option>
+      <option value="danio_rerio">danio_rerio</option>
+      <option value="mastacembelus_armatus">mastacembelus_armatus</option>
+      <option value=""></option>
+    </param>
+    <param name="species_type" type="select" label="Get the Ensembl, Refseq or merged Ensembl/Refseq">
+      <option value="ensembl" selected="true">Ensembl</option>
+      <option value="refseq">Refseq</option>
+      <option value="merged">Merged</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file" format="data_manager_json"/>
+  </outputs>
+  <!-- 
+  <tests>
+      <test>
+          DON'T FORGET TO DEFINE SOME TOOL TESTS
+      </test>
+  </tests>
+  -->
+  <help>
+  There is no help
+  </help>
+</tool>