Merge pull request #1451 from bebatut/enasearch

Add ENASearch

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.

tools/enasearch/README.md

@@ -0,0 +1,11 @@
+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
+```

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>

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>

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>

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>

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>