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Add ENASearch #1451

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merged 16 commits into from
Aug 29, 2017
Merged

Add ENASearch #1451

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791d222
enasearch_retrieve_analysis_report: add wrapper
bebatut Aug 5, 2017
4fdfa0b
enasearch_retrieve_analysis_report: fix name
bebatut Aug 8, 2017
a056b8b
enasearch_retrieve_data: add wrapper
bebatut Aug 8, 2017
1a29bf9
enasearch_retrieve_run_report: add wrapper
bebatut Aug 8, 2017
4ac76f0
Extend the use of macros
bebatut Aug 8, 2017
50b62c7
enasearch_retrieve_taxons: add wrapper
bebatut Aug 8, 2017
4b78927
enasearch_search_data: add wrapper
bebatut Aug 8, 2017
c4dfc5b
enasearch_search_data: Fix some macros errors
bebatut Aug 9, 2017
4234a70
Fix expanded and header
bebatut Aug 25, 2017
5a1b15e
Update enasearch version
bebatut Aug 28, 2017
94d91b9
enasearch_search_data: fix format change
bebatut Aug 28, 2017
e388424
Fix the tests
bebatut Aug 28, 2017
43ab9bb
enasearch_search_data: remove extra quotes
bebatut Aug 28, 2017
b35d162
Fix flake8 linting
bebatut Aug 28, 2017
5429c3a
Add readme file
bebatut Aug 28, 2017
a8b99e5
Add .shed.yml file
bebatut Aug 29, 2017
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18 changes: 18 additions & 0 deletions tools/enasearch/.shed.yml
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name: enasearch
owner: iuc
description: "A Python library for interacting with ENA's API"
homepage_url: https://github.com/bebatut/enasearch
long_description: |
ENASearch is a Python library for interacting with ENA's API.
remote_repository_url: https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/
type: unrestricted
categories:
- Data Source
auto_tool_repositories:
name_template: "{{ tool_id }}"
description_template: "Wrapper for the ENASearch tool suite: {{ tool_name }}"
suite:
name: "suite_enasearch"
description: "A Python library for interacting with ENA's API"
long_description: |
ENASearch is a Python library for interacting with ENA's API.
11 changes: 11 additions & 0 deletions tools/enasearch/README.md
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ENASearch
=========

[ENASearch](https://github.com/bebatut/enasearch) is a Python library for interacting with [ENA](http://www.ebi.ac.uk/ena/browse/programmatic-access)'s API.

For any change in the `macros.xml`, please change on [`generate_macros.py`](generate_macros.py) and regenerate the `macros.xml` with

```
$ conda install enasearch
$ python generate_macros.py
```
47 changes: 47 additions & 0 deletions tools/enasearch/enasearch_retrieve_analysis_report.xml
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<tool id="enasearch_retrieve_analysis_report" name="Retrieve an analysis report" version="@WRAPPER_VERSION@.0">
<description></description>
<macros>
<import>macros.xml</import>
<import>search_macros.xml</import>
</macros>
<expand macro="requirements"/>
<expand macro="version"/>
<command detect_errors="aggressive"><![CDATA[
enasearch
retrieve_analysis_report
--accession '$accession'
@FIELDS@
--file '$output'
]]></command>
<inputs>
<expand macro="accession"/>
<param argument="--fields" type="select" optional="true" multiple="true" label="Fields to return">
<expand macro="analysis_fields"/>
</param>
</inputs>
<outputs>
<data name="output" format="tabular" label="${tool.name} on ${accession}"/>
</outputs>
<tests>
<test>
<param name="accession" value="ERZ009929"/>
<output name="output" md5="cfcb3fb4db26e039f12f36eaa7519871"/>
</test>
<test>
<param name="accession" value="ERZ009929"/>
<param name="fields" value="analysis_accession"/>
<output name="output" md5="7249f93fac05d1e6746a076e1ae445b5"/>
</test>
<test>
<param name="accession" value="ERZ009929"/>
<param name="fields" value="analysis_accession,sample_accession,scientific_name"/>
<output name="output" md5="af4ba9b125b27525979ab6ea6a2b3637"/>
</test>
</tests>
<help><![CDATA[
**What it does**

This tool retrieve an analysis report for an accession id
]]></help>
<expand macro="citations"/>
</tool>
72 changes: 72 additions & 0 deletions tools/enasearch/enasearch_retrieve_data.xml
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<tool id="enasearch_retrieve_data" name="Retrieve ENA data" version="@WRAPPER_VERSION@.0">
<description>(other than taxon and project)</description>
<macros>
<import>macros.xml</import>
<import>search_macros.xml</import>
</macros>
<expand macro="requirements"/>
<expand macro="version"/>
<command detect_errors="aggressive"><![CDATA[
enasearch
retrieve_data
@IDS@
@DISPLAY@
$expanded
$header
--file '$output'
--download 'txt'
]]></command>
<inputs>
<param argument="--ids" type="text" multiple="true" label="Ids for records to return" help="Other than Taxon and Project. It can also be range of ids (e.g. ERA000010-ERA000020)"/>
<expand macro="display_opt"/>
<expand macro="expanded"/>
<expand macro="header"/>
</inputs>
<outputs>
<data name="output" format="tabular" label="${tool.name} on ${ids}">
<expand macro="change_format"/>
</data>
</outputs>
<tests>
<test>
<param name="ids" value="ERA000010-ERA000020"/>
<conditional name="display_opt">
<param name="display" value="xml"/>
</conditional>
<output name="output" ftype="xml" md5="d42dec30c41578705ba9b167dc0c30b1"/>
</test>
<test>
<param name="ids" value="A00145"/>
<conditional name="display_opt">
<param name="display" value="fasta"/>
<param name="range_start" value="3"/>
<param name="range_stop" value="63"/>
</conditional>
<output name="output" ftype="fasta" md5="758cb77161dcf6f8cf841cb141e9277e"/>
</test>
<test>
<param name="ids" value="AL513382"/>
<conditional name="display_opt">
<param name="display" value="text"/>
<param name="offset" value="0"/>
<param name="length" value="100"/>
</conditional>
<param name="expanded" value="true"/>
<output name="output" md5="e77ed0fb6f75093251b6ddc98f9db835"/>
</test>
<test>
<param name="ids" value="PRJEB2772,AL513382"/>
<conditional name="display_opt">
<param name="display" value="html"/>
</conditional>
<param name="header" value="true"/>
<output name="output" md5="7b23a8c12893728272f4993073e341f6"/>
</test>
</tests>
<help><![CDATA[
**What it does**

This tool retrieve ENA data (other than taxon and project)
]]></help>
<expand macro="citations"/>
</tool>
42 changes: 42 additions & 0 deletions tools/enasearch/enasearch_retrieve_run_report.xml
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<tool id="enasearch_retrieve_run_report" name="Retrieve a run report" version="@WRAPPER_VERSION@.0">
<description></description>
<macros>
<import>macros.xml</import>
<import>search_macros.xml</import>
</macros>
<expand macro="requirements"/>
<expand macro="version"/>
<command detect_errors="aggressive"><![CDATA[
enasearch
retrieve_run_report
--accession '$accession'
@FIELDS@
--file '$output'
]]></command>
<inputs>
<expand macro="accession"/>
<param argument="--fields" type="select" optional="true" multiple="true" label="Fields to return">
<expand macro="run_fields"/>
</param>
</inputs>
<outputs>
<data name="output" format="tabular" label="${tool.name} on ${accession}"/>
</outputs>
<tests>
<test>
<param name="accession" value="SRX017289"/>
<output name="output" md5="0f0c6df8d03b9b26b2906921524d7ad1"/>
</test>
<test>
<param name="accession" value="SRX017289"/>
<param name="fields" value="study_accession,study_title,sra_aspera"/>
<output name="output" md5="c6e42cb421832aafac42de4bfc9cc7e8"/>
</test>
</tests>
<help><![CDATA[
**What it does**

This tool retrieve a run report for an accession id
]]></help>
<expand macro="citations"/>
</tool>
59 changes: 59 additions & 0 deletions tools/enasearch/enasearch_retrieve_taxons.xml
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<tool id="enasearch_retrieve_taxons" name="Retrieve ENA taxon data" version="@WRAPPER_VERSION@.0">
<description></description>
<macros>
<import>macros.xml</import>
<import>search_macros.xml</import>
</macros>
<expand macro="requirements"/>
<expand macro="version"/>
<command detect_errors="aggressive"><![CDATA[
enasearch
retrieve_taxons
@IDS@
#if $result
--result '$result'
#end if
@DISPLAY@
$expanded
$header
--file '$output'
--download 'txt'
]]></command>
<inputs>
<param argument="--ids" type="text" multiple="true" label="Ids for records to return"/>
<param argument="--result" type="select" optional="true" label="Taxonomy result to return">
<expand macro="taxonomy_results"/>
</param>
<expand macro="display_opt"/>
<expand macro="expanded"/>
<expand macro="header"/>
</inputs>
<outputs>
<data name="output" format="tabular" label="${tool.name} on ${ids}">
<expand macro="change_format"/>
</data>
</outputs>
<tests>
<test>
<param name="ids" value="6543"/>
<param name="result" value="sequence_release"/>
<conditional name="display_opt">
<param name="display" value="fasta"/>
</conditional>
<output name="output" ftype="fasta" md5="e2fe353d00ffdec2f8b884903add458b"/>
</test>
<test>
<param name="ids" value="Human,Cat,Mouse,Zebrafish"/>
<conditional name="display_opt">
<param name="display" value="xml"/>
</conditional>
<output name="output" ftype="xml" md5="0833f5ac248a3e7f382e4d53762fc71d"/>
</test>
</tests>
<help><![CDATA[
**What it does**

This tool retrieve ENA taxon data
]]></help>
<expand macro="citations"/>
</tool>
143 changes: 143 additions & 0 deletions tools/enasearch/enasearch_search_data.xml
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<tool id="enasearch_search_data" name="Search ENA data" version="@WRAPPER_VERSION@.0">
<description>given a query</description>
<macros>
<import>macros.xml</import>
<import>search_macros.xml</import>
</macros>
<expand macro="requirements"/>
<expand macro="version"/>
<command detect_errors="aggressive"><![CDATA[
enasearch
search_data
$query_type.free_text_search
#if $query_type.free_text_search == '--free_text_search'
--query '$query_type.query'
--result '$query_type.res.result'
@SEARCH_DATA_DISPLAY@
#else
--result '$query_type.res.result'
#set $queries=''
#set $sep=''
#for $i, $s in enumerate( $query_type.res.queries )
#if $sep == ''
#set $sep = str($s.combination_operation)
#else
#set $sep = str($s.combination_operation)
#set $queries += ' %s ' % ($sep)
#end if
#if $s.filter_field.field != 'location'
#set $queries += '%s' % (str($s.filter_field.field))
#if str($s.filter_field.operation) == "equal"
#set $queries += '='
#elif str($s.filter_field.operation) == "different"
#set $queries += '!='
#elif str($s.filter_field.operation) == "lower"
#set $queries += '<'
#elif str($s.filter_field.operation) == "equal or lower"
#set $queries += '<='
#elif str($s.filter_field.operation) == "higher"
#set $queries += '>'
#elif str($s.filter_field.operation) == "equal or higher"
#set $queries += '>='
#end if
#set $queries += '"%s"' % (str($s.filter_field.value))
#else
#set $queries += '%s(%s)' % (str($s.filter_field.operation),str($s.filter_field.values))
#end if
#end for
--query '$queries'
@SEARCH_DATA_DISPLAY@
#end if
--file '$output'
--download 'txt'
]]></command>
<inputs>
<conditional name="query_type">
<param argument="--free_text_search" type="select" label="Use free text search?" help="If not, the ENA data warehouse is used">
<option value="--free_text_search">Yes</option>
<option value="">False</option>
</param>
<when value="--free_text_search">
<param argument="--query" type="text" label="Query"/>
<expand macro="free_text_search"/>
</when>
<when value="">
<expand macro="conditional_text_search"/>
</when>
</conditional>
</inputs>
<outputs>
<data name="output" format="tabular" label="${tool.name}">
<change_format>
<when input="query_type.res.display_opt.display" value="fasta" format="fasta" />
<when input="query_type.res.display_opt.display" value="fastq" format="fastq" />
<when input="query_type.res.display_opt.display" value="html" format="html" />
<when input="query_type.res.display_opt.display" value="text" format="text" />
<when input="query_type.res.display_opt.display" value="xml" format="xml" />
</change_format>
</data>
</outputs>
<tests>
<test>
<conditional name="query_type">
<param name="free_text_search" value="--free_text_search"/>
<param name="query" value="kinase+homo+sapiens"/>
<conditional name="res">
<param name="result" value="sequence_update"/>
<conditional name="display_opt">
<param name="display" value="fasta"/>
</conditional>
</conditional>
</conditional>
<output name="output" ftype="fasta" md5="d02da99308bbf1e432fc5614c1982994"/>
</test>
<test>
<conditional name="query_type">
<param name="free_text_search" value="--free_text_search"/>
<param name="query" value="kinase+homo+sapiens"/>
<conditional name="res">
<param name="result" value="wgs_set"/>
<conditional name="display_opt">
<param name="display" value="report"/>
<param name="fields" value="accession,environmental_sample"/>
</conditional>
</conditional>
</conditional>
<output name="output" ftype="tabular" md5="c1f91a8276f59c90ec53025e1a3d31d5"/>
</test>
<test>
<conditional name="query_type">
<param name="free_text_search" value=""/>
<conditional name="res">
<param name="result" value="coding_release"/>
<repeat name="queries">
<param name="combination_operation" value="AND"/>
<conditional name="filter_field">
<param name="field" value="dataclass"/>
<param name="operation" value="equal"/>
<param name="value" value="STD"/>
</conditional>
</repeat>
<repeat name="queries">
<param name="combination_operation" value="AND"/>
<conditional name="filter_field">
<param name="field" value="tissue_lib"/>
<param name="operation" value="equal"/>
<param name="value" value="lambda gt11"/>
</conditional>
</repeat>
<conditional name="display_opt">
<param name="display" value="xml"/>
</conditional>
</conditional>
</conditional>
<output name="output" ftype="xml" md5="0ed405b4db2bcaf9c1540307fe15e9bb"/>
</test>
</tests>
<help><![CDATA[
**What it does**

This tool retrieve ENA taxon data
]]></help>
<expand macro="citations"/>
</tool>