diff esearch.xml @ 0:c8a84e910e6b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/esearch.xml	Thu Jul 07 02:40:48 2016 -0400
@@ -0,0 +1,155 @@
+<?xml version="1.0"?>
+<tool id="ncbi_eutils_esearch" name="NCBI ESearch" version="@WRAPPER_VERSION@">
+  <description>search NCBI Databases by text query</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <version_command>python esearch.py --version</version_command>
+  <command detect_errors="aggressive" interpreter="python"><![CDATA[esearch.py
+$db_select
+"$term"
+
+#if $history_file and $history_file is not None:
+    --history_file $history_file
+#end if
+
+#if $date.enabled:
+    --datetype $date.datetype
+
+    #if $date.reldate and $date.reldate is not None:
+    --reldate $date.reldate
+    #end if
+
+    #if $date.mindate and $date.mindate is not None:
+    --mindate $date.mindate
+    #end if
+
+    #if $date.maxdate and $date.maxdate is not None:
+    --maxdate $date.maxdate
+    #end if
+#end if
+
+#if $use_history:
+    --history_out $history
+#end if
+
+@EMAIL_ARGUMENTS@
+> $default]]></command>
+  <inputs>
+    <expand macro="dbselect"/>
+    <param label="Search Term" name="term" type="text">
+      <sanitizer>
+        <valid>
+          <add value="'"/>
+          <add value="["/>
+          <add value="]"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param label="Filter existing history" name="history_file" type="data" format="json" optional="True"/>
+    <param checked="false" label="Store results to history server" name="use_history" type="boolean" truevalue="--use_history" falsevalue=""/>
+    <conditional name="date">
+      <param label="Filter By Date" type="boolean" truevalue="True" falsevalue="False" checked="false" name="enabled"/>
+      <when value="True">
+        <param label="Date type" name="datetype" type="select">
+          <option value="PDAT">Publish Date</option>
+          <option value="EDAT">Entrez Date</option>
+          <option value="MDAT">Modification Date</option>
+        </param>
+        <param label="In past N days" name="reldate" type="integer" min="1" optional="True"/>
+        <param label="Minimum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="mindate" type="text"/>
+        <param label="maximum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="maxdate" type="text"/>
+      </when>
+      <when value="False"/>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="json" name="default" label="ESearch Results for $term">
+      <change_format>
+        <when input="use_history" value="" format="xml"/>
+      </change_format>
+    </data>
+    <expand macro="history_out">
+      <filter>use_history</filter>
+    </expand>
+  </outputs>
+  <tests>
+    <test>
+      <param name="db_select" value="pubmed"/>
+      <param name="term" value="(PNAS[ta] AND 97[vi])"/>
+      <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/>
+    </test>
+    <test>
+      <param name="db_select" value="pubmed"/>
+      <param name="term" value="PNAS[ta]"/>
+      <param name="enabled" value="True"/>
+      <param name="datetype" value="PDAT"/>
+      <param name="mindate" value="2014/01/01"/>
+      <param name="maxdate" value="2014/02/01"/>
+      <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+NCBI Entrez ESearch
+===================
+
+Responds to a text query with the list of matching UIDs in a given database
+(for later use in ESummary, EFetch or ELink), along with the term translations
+of the query.
+
+Example Queries
+---------------
+
+Search in PubMed with the term cancer for abstracts that have an Entrez date
+within the last 60 days:
+
++----------------------+-------------+
+| Parameter            | Value       |
++======================+=============+
+| NCBI Database to Use | PubMed      |
++----------------------+-------------+
+| Term                 | Cancer      |
++----------------------+-------------+
+| Datetype             | Entrez Date |
++----------------------+-------------+
+| In past N Days       | 60          |
++----------------------+-------------+
+
+Search PubMed Central for free full text articles containing the query stem cells:
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| NCBI Database to Use | PubMedCentral                        |
++----------------------+--------------------------------------+
+| Term                 | Stem Cells AND free fulltext[filter] |
++----------------------+--------------------------------------+
+
+Search in Nucleotide for all tRNAs:
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| NCBI Database to Use | Nucleotide                           |
++----------------------+--------------------------------------+
+| Term                 | biomol trna[prop]                    |
++----------------------+--------------------------------------+
+
+Search in Protein for a molecular weight range:
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| NCBI Database to Use | Protein                              |
++----------------------+--------------------------------------+
+| Term                 | 70000:90000[molecular weight]        |
++----------------------+--------------------------------------+
+
+
+@REFERENCES@
+
+@DISCLAIMER@
+      ]]></help>
+  <expand macro="citations"/>
+</tool>