| Previous changeset 1:a2c83f79f253 (2016-12-12) Next changeset 3:42d5e40fcd0b (2017-02-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba |
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modified:
ebeye_urllib.py generate_macros.py macros.xml |
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| diff -r a2c83f79f253 -r b6029f2c71cb ebeye_urllib.py --- a/ebeye_urllib.py Mon Dec 12 10:04:11 2016 -0500 +++ b/ebeye_urllib.py Sat Jan 21 14:41:05 2017 -0500 |
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| @@ -5,19 +5,16 @@ # and distributed under the Apache License # ====================================================================== # Load libraries +import os import platform -import os +import re import urllib -import re +import urllib2 +from gzip import GzipFile from optparse import OptionParser -from gzip import GzipFile +from StringIO import StringIO + from xmltramp2 import xmltramp -# python2 -from StringIO import StringIO -import urllib2 -# python3 -# import urllib.request as urllib2 - # Service base URL baseUrl = 'http://www.ebi.ac.uk/ebisearch/ws/rest' |
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| diff -r a2c83f79f253 -r b6029f2c71cb generate_macros.py --- a/generate_macros.py Mon Dec 12 10:04:11 2016 -0500 +++ b/generate_macros.py Sat Jan 21 14:41:05 2017 -0500 |
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| @@ -16,10 +16,10 @@ def add_select_parameter(name, label, multiple=False): to_write = '<param ' to_write += 'name="%s" ' % (name) - to_write += 'type="select" ' - to_write += 'label="%s" ' % (label) + to_write += 'type="select"' if multiple: - to_write += 'multiple=\"true\"' + to_write += ' multiple="true" optional="false"' + to_write += ' label="%s"' % (label) to_write += '>\n' return to_write @@ -30,6 +30,7 @@ to_write += '%s<xml name="requirements">\n' % (spaces) to_write += '%s<requirements>\n' % (2 * spaces) + to_write += '%s<requirement type="package" version="2.7.12">python</requirement>\n' % (3 * spaces) to_write += '%s<requirement type="package" version="3.1.1">xmltramp2</requirement>\n' % (3 * spaces) to_write += '%s<requirement type="package" version="1.12">urllib3</requirement>\n' % (3 * spaces) to_write += '%s<yield/>\n' % (3 * spaces) @@ -44,7 +45,7 @@ 'Domain to query')) sorted_domains = [(d, domains_fields[d]['name']) for d in domains_fields.keys()] - sorted_domains = sorted(sorted_domains, key=lambda tup: tup[1]) + sorted_domains.sort(key=lambda tup: tup[1]) for domain in sorted_domains: to_write += '%s%s' % (4 * spaces, add_option( domain[0], @@ -65,7 +66,6 @@ field, field, selected=True)) - to_write += '%s<validator type="no_options" message="Please select at least one field" />\n' % (5 * spaces) to_write += '%s</param>\n' % (4 * spaces) to_write += '%s<repeat name="queries" title="Add a query">\n' % ( |
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| diff -r a2c83f79f253 -r b6029f2c71cb macros.xml --- a/macros.xml Mon Dec 12 10:04:11 2016 -0500 +++ b/macros.xml Sat Jan 21 14:41:05 2017 -0500 |
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| b'@@ -9,7 +9,7 @@\n </xml>\n <xml name="inputs">\n <conditional name="searched_domain">\n- <param name="domain" type="select" label="Domain to query" >\n+ <param name="domain" type="select" label="Domain to query">\n <option value="sra-analysis">Analysis</option>\n <option value="arrayexpress-repository">ArrayExpress</option>\n <option value="genome_assembly">Assembly</option>\n@@ -122,7 +122,7 @@\n </param>\n \n <when value="sra-analysis">\n- <param name="fields" type="select" label="Fields to extract" multiple="true">\n+ <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract">\n <option value="PROJECT" selected="true">PROJECT</option>\n <option value="PUBMED" selected="true">PUBMED</option>\n <option value="SRA-STUDY" selected="true">SRA-STUDY</option>\n@@ -130,15 +130,14 @@\n <option value="description" selected="true">description</option>\n <option value="domain_source" selected="true">domain_source</option>\n <option value="id" selected="true">id</option>\n- <validator type="no_options" message="Please select at least one field" />\n- </param>\n- <repeat name="queries" title="Add a query">\n- <param name="combination_operation" type="select" label="Combination operation" >\n- <option value="AND">AND</option>\n- <option value="OR">OR</option>\n- <option value="NOT">NOT</option>\n- </param>\n- <param name="query_field" type="select" label="Fields" >\n+ </param>\n+ <repeat name="queries" title="Add a query">\n+ <param name="combination_operation" type="select" label="Combination operation">\n+ <option value="AND">AND</option>\n+ <option value="OR">OR</option>\n+ <option value="NOT">NOT</option>\n+ </param>\n+ <param name="query_field" type="select" label="Fields">\n <option value="PROJECT">PROJECT</option>\n <option value="PUBMED">PUBMED</option>\n <option value="SRA-STUDY">SRA-STUDY</option>\n@@ -152,7 +151,7 @@\n <option value="id">id</option>\n </param>\n <conditional name="comp_operation">\n- <param name="operation" type="select" label="Comparison operation" >\n+ <param name="operation" type="select" label="Comparison operation">\n <option value="equal">equal</option>\n <option value="not">not</option>\n <option value="range">range</option>\n@@ -173,7 +172,7 @@\n </when>\n \n <when value="arrayexpress-repository">\n- <param name="fields" type="select" label="Fields to extract" multiple="true">\n+ <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract">\n <option value="PUBMED" selected="true">PUBMED</option>\n <option value="TAXONOMY" selected="true">TAXONOMY</option>\n <option value="data_protocol" selected="true">data_protocol</option>\n@@ -191,15 +190,14 @@\n <option value="submission_date" selected="true">submission_date</option>\n <option value="submitter_keywords" selected="true">submitter_keywords</option>\n <option value="tissue" selected="true">tissue</option>\n- <validator type="no_options" message="Please select at least one field" />\n- </param>\n- '..b'>NOT</option>\n- </param>\n- <param name="query_field" type="select" label="Fields" >\n+ </param>\n+ <repeat name="queries" title="Add a query">\n+ <param name="combination_operation" type="select" label="Combination operation">\n+ <option value="AND">AND</option>\n+ <option value="OR">OR</option>\n+ <option value="NOT">NOT</option>\n+ </param>\n+ <param name="query_field" type="select" label="Fields">\n <option value="TAXONOMY">TAXONOMY</option>\n <option value="UNIPARC">UNIPARC</option>\n <option value="UNIPROT">UNIPROT</option>\n@@ -9219,7 +9111,7 @@\n <option value="name">name</option>\n </param>\n <conditional name="comp_operation">\n- <param name="operation" type="select" label="Comparison operation" >\n+ <param name="operation" type="select" label="Comparison operation">\n <option value="equal">equal</option>\n <option value="not">not</option>\n <option value="range">range</option>\n@@ -9240,7 +9132,7 @@\n </when>\n \n <when value="wormbaseParasite">\n- <param name="fields" type="select" label="Fields to extract" multiple="true">\n+ <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract">\n <option value="ARRAYEXPRESS" selected="true">ARRAYEXPRESS</option>\n <option value="EMBL" selected="true">EMBL</option>\n <option value="ENSEMBL_ORTHOLOG" selected="true">ENSEMBL_ORTHOLOG</option>\n@@ -9290,15 +9182,14 @@\n <option value="system_name" selected="true">system_name</option>\n <option value="transcript" selected="true">transcript</option>\n <option value="transcript_count" selected="true">transcript_count</option>\n- <validator type="no_options" message="Please select at least one field" />\n- </param>\n- <repeat name="queries" title="Add a query">\n- <param name="combination_operation" type="select" label="Combination operation" >\n- <option value="AND">AND</option>\n- <option value="OR">OR</option>\n- <option value="NOT">NOT</option>\n- </param>\n- <param name="query_field" type="select" label="Fields" >\n+ </param>\n+ <repeat name="queries" title="Add a query">\n+ <param name="combination_operation" type="select" label="Combination operation">\n+ <option value="AND">AND</option>\n+ <option value="OR">OR</option>\n+ <option value="NOT">NOT</option>\n+ </param>\n+ <param name="query_field" type="select" label="Fields">\n <option value="ARRAYEXPRESS">ARRAYEXPRESS</option>\n <option value="EMBL">EMBL</option>\n <option value="ENSEMBL_ORTHOLOG">ENSEMBL_ORTHOLOG</option>\n@@ -9353,7 +9244,7 @@\n <option value="transcript">transcript</option>\n </param>\n <conditional name="comp_operation">\n- <param name="operation" type="select" label="Comparison operation" >\n+ <param name="operation" type="select" label="Comparison operation">\n <option value="equal">equal</option>\n <option value="not">not</option>\n <option value="range">range</option>\n' |