Mercurial > repos > matthias > data_manager_megan_tools

changeset 0:1f839ba466da draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
author matthias
date Thu, 01 Nov 2018 12:25:53 -0400
parents
children f7ad11d31098
files data_manager/.megan_tools_fetcher.xml.swp data_manager/data_manager.py data_manager/megan_tools_fetcher.xml data_manager_conf.xml test-data/SSURef_Nr99_132_tax_silva_to_NCBI_synonyms_json tool-data/megan_tools.loc.sample tool_data_table_conf.xml.sample
diffstat 5 files changed, 192 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
Binary file data_manager/.megan_tools_fetcher.xml.swp has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager.py	Thu Nov 01 12:25:53 2018 -0400
@@ -0,0 +1,103 @@
+import argparse
+import datetime
+import json
+import os
+import shutil
+import tarfile
+import zipfile
+try:
+    # For Python 3.0 and later
+    from urllib.request import Request, urlopen
+except ImportError:
+    # Fall back to Python 2 imports
+    from urllib2 import Request, urlopen
+
+FILE2NAME = {
+    "prot_acc2tax-June2018X1.abin.zip":"Protein accession to NCBI-taxonomy (June2018X1)",
+    "nucl_acc2tax-June2018.abin.zip":"Nucleotide accession to NCBI-taxonomy (June2018)",
+    "acc2interpro-June2018X.abin.zip":"Protein accession to InterPro (June2018X)",
+    "acc2eggnog-Oct2016X.abin.zip":"Protein accession to eggNOG (Oct2016X)",
+    "acc2seed-May2015XX.abin.zip":"Protein accession to SEED (May2015XX)",
+    "acc2kegg-Dec2017X1-ue.abin.zip":"Protein accession to KEGG (Dec2017X1). Only for use with the Ultimate Edition of MEGAN.",
+    "SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz":"SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz",
+    "SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz":"SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz",
+    "prot_gi2tax-Aug2016X.bin.zip":"Protein accession to NCBI-taxonomy (Aug2016X)",
+    "nucl_gi2tax-Aug2016.bin.zip":"Nucleotide accession to NCBI-taxonomy (Aug2016)",
+    "gi2eggnog-June2016X.bin.zip":"Protein accession to InterPro (June2016X)",
+    "gi2interpro-June2016X.bin.zip":"Protein accession to eggNOG (June2016X)",
+    "gi2seed-May2015X.bin.zip":"Protein accession to SEED (May2015X)",
+    "gi2kegg-Aug2016X-ue.bin.zip":"Protein accession to KEGG (Aug2016X). Only for use with the Ultimate Edition of MEGAN."
+}
+
+FILE2TYPE = {
+    "prot_acc2tax-June2018X1.abin.zip":"acc2tax",
+    "nucl_acc2tax-June2018.abin.zip":"acc2tax",
+    "acc2interpro-June2018X.abin.zip":"acc2interpro",
+    "acc2eggnog-Oct2016X.abin.zip":"acc2eggnog",
+    "acc2seed-May2015XX.abin.zip":"acc2seed",
+    "acc2kegg-Dec2017X1-ue.abin.zip":"acc2kegg",
+    "SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz":"syn2taxa",
+    "SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz":"syn2taxa",
+    "prot_gi2tax-Aug2016X.bin.zip":"gi2tax",
+    "nucl_gi2tax-Aug2016.bin.zip":"gi2tax",
+    "gi2eggnog-June2016X.bin.zip":"gi2eggnog",
+    "gi2interpro-June2016X.bin.zip":"gi2interpro",
+    "gi2seed-May2015X.bin.zip":"gi2seed-",
+    "gi2kegg-Aug2016X-ue.bin.zip":"gi2kegg"
+}
+
+def url_download(fname, workdir):
+    file_path = os.path.join(workdir, 'download.dat')
+    if not os.path.exists(workdir):
+        os.makedirs(workdir)
+    src = None
+    dst = None
+    try:
+        req = Request("http://ab.inf.uni-tuebingen.de/data/software/megan6/download/"+fname)
+        src = urlopen(req)
+        with open(file_path, 'wb') as dst:
+            while True:
+                chunk = src.read(2**10)
+                if chunk:
+                    dst.write(chunk)
+                else:
+                    break
+    finally:
+        if src:
+            src.close()
+    if zipfile.is_zipfile(file_path):
+        fh = zipfile.ZipFile(file_path, 'r')
+    else:
+        return
+    fh.extractall(workdir)
+    os.remove(file_path)
+
+
+def main(fname, outjson):
+    workdir = os.path.join(os.getcwd(), 'megan_tools')
+    url_download(fname, workdir)
+
+    data_manager_entry = {}
+    data_manager_entry['value'] = fname.split(".")[0]
+    data_manager_entry['name'] = FILE2NAME[fname]
+    data_manager_entry['type'] = FILE2TYPE[fname]
+    data_manager_entry['path'] = '.'
+
+    data_manager_json = dict(data_tables=dict(megan_tools=data_manager_entry))
+
+    params = json.loads(open(outjson).read())
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_directory)
+    output_path = os.path.abspath(os.path.join(os.getcwd(), 'megan_tools'))
+    for filename in os.listdir(workdir):
+        shutil.move(os.path.join(output_path, filename), target_directory)
+    file(outjson, 'w').write(json.dumps(data_manager_json))
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Create data manager json.')
+    parser.add_argument('--out', action='store', help='JSON filename')
+    parser.add_argument('--file', action='store', help='Download filename')
+    args = parser.parse_args()
+
+    main(args.file, args.out)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/megan_tools_fetcher.xml	Thu Nov 01 12:25:53 2018 -0400
@@ -0,0 +1,62 @@
+<?xml version="1.0"?>
+<tool id="megan_tools_fetcher" name="megan tools" tool_type="manage_data" version="0.0.1">
+    <description>Mapping files downloader</description>
+    <command detect_errors="exit_code">
+    <![CDATA[
+    python '$__tool_directory__/data_manager.py' 
+    --out '${out_file}'
+    --file '$type_cond.database_name'
+    ]]>
+    </command>
+    <inputs>
+        <conditional name="type_cond">
+            <param name="type_select" type="select" label="mapping type">
+                <option value="ncbi_current">Mapping files for current NCBI-nr protein database (not containing GI numbers)</option>
+                <option value="silva">Mapping file for working with the SILVA SSU database</option>
+                <option value="ncbi_deprecated">Deprecated mapping files for NCBI-nr protein database (releases until August 2016, containing GI numbers):</option>
+	    </param>
+            <when value="ncbi_current">
+                <param name="database_name" type="select" label="mapping data">
+                    <option value="prot_acc2tax-June2018X1.abin.zip">Protein accession to NCBI-taxonomy (June2018X1)</option>
+                    <option value="nucl_acc2tax-June2018.abin.zip">Nucleotide accession to NCBI-taxonomy (June2018)</option>
+                    <option value="acc2interpro-June2018X.abin.zip">Protein accession to InterPro (June2018X)</option>
+                    <option value="acc2eggnog-Oct2016X.abin.zip">Protein accession to eggNOG (Oct2016X)</option>
+                    <option value="acc2seed-May2015XX.abin.zip">Protein accession to SEED (May2015XX)</option>
+                    <option value="acc2kegg-Dec2017X1-ue.abin.zip">Protein accession to KEGG (Dec2017X1). Only for use with the Ultimate Edition of MEGAN.</option>
+                </param>
+            </when>
+            <when value="silva">
+                <param name="database_name" type="select" label="mapping data">
+                    <option value="SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz">SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz</option>
+                    <option value="SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz">SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz</option>
+                </param>
+            </when>
+            <when value="ncbi_deprecated">
+                <param name="database_name" type="select" label="mapping data">
+                    <option value="prot_gi2tax-Aug2016X.bin.zip">Protein accession to NCBI-taxonomy (Aug2016X)</option>
+                    <option value="nucl_gi2tax-Aug2016.bin.zip">Nucleotide accession to NCBI-taxonomy (Aug2016)</option>
+                    <option value="gi2eggnog-June2016X.bin.zip">Protein accession to InterPro (June2016X)</option>
+                    <option value="gi2interpro-June2016X.bin.zip">Protein accession to eggNOG (June2016X)</option>
+                    <option value="gi2seed-May2015X.bin.zip">Protein accession to SEED (May2015X)</option>
+                    <option value="gi2kegg-Aug2016X-ue.bin.zip">Protein accession to KEGG (Aug2016X). Only for use with the Ultimate Edition of MEGAN.</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="type_cond">
+                <param name="type_select" value="silva"/>
+                <param name="database_name" value="SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz"/>
+            </conditional>
+            <output name="out_file" file="SSURef_Nr99_132_tax_silva_to_NCBI_synonyms_json"/>
+        </test>
+    </tests>
+    <help>
+TODO
+    </help>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Thu Nov 01 12:25:53 2018 -0400
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/megan_tools_fetcher.xml" id="megan_tools_fetcher" version="0.0.1">
+        <data_table name="megan_tools">
+            <output>
+                <column name="value" />
+                <column name="name" />
+                <column name="type" />
+                <column name="path" output_ref="out_file">
+                    <move type="directory" relativize_symlinks="True">
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">megan_tools/${value}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/megan_tools/${value}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Nov 01 12:25:53 2018 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of data downloaded for the megan tools -->
+    <table name="megan_tools" comment_char="#">
+        <columns>value, name, type, path</columns>
+        <file path="tool-data/megan_tools.loc" />
+    </table>
+</tables>