diff efetch.xml @ 0:71bcf87a7031 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/efetch.xml	Thu Jul 07 02:39:36 2016 -0400
@@ -0,0 +1,83 @@
+<?xml version="1.0"?>
+<tool id="ncbi_eutils_efetch" name="NCBI EFetch" version="@WRAPPER_VERSION@">
+  <description>fetch records from NCBI</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <version_command>python efetch.py --version</version_command>
+  <command detect_errors="aggressive" interpreter="python"><![CDATA[efetch.py
+$db.db_select
+
+@LIST_OR_HIST@
+
+#set rettype, retmode = str($db.output_format).split('-')
+## Otherwise, defaults to a None/empty which implies 'default' to NCBI
+#if retmode != "null":
+--retmode $retmode
+#end if
+--rettype $rettype
+
+@EMAIL_ARGUMENTS@
+]]></command>
+  <inputs>
+    <expand macro="db"/>
+    <expand macro="list_or_hist"/>
+  </inputs>
+  <outputs>
+    <collection type="list" label="NCBI EFetch Results" name="output1">
+      <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
+    </collection>
+  </outputs>
+  <tests>
+    <test>
+      <param name="db_select" value="taxonomy"/>
+      <param name="output_format" value="full-xml"/>
+      <param name="qss" value="id_list"/>
+      <param name="id_list" value="10239"/>
+      <output name="default">
+        <discovered_dataset designation="EFetch Results Chunk 0" ftype="xml" file="viruses.tax.xml" lines_diff="2">
+        </discovered_dataset>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[
+NCBI Entrez EFetch
+==================
+
+Responds to a list of UIDs in a given database with the corresponding data
+records in a specified format.
+
+Example Queries
+---------------
+
+Fetch PMIDs 17284678 and 9997 as text abstracts:
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| NCBI Database to Use | PubMed                               |
++----------------------+--------------------------------------+
+| ID List              | 17284678 9997                        |
++----------------------+--------------------------------------+
+| Output Format        | Abstract                             |
++----------------------+--------------------------------------+
+
+Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| NCBI Database to Use | Protein                              |
++----------------------+--------------------------------------+
+| ID List              | 312836839 34577063                   |
++----------------------+--------------------------------------+
+| Output Format        | Fasta                                |
++----------------------+--------------------------------------+
+
+@REFERENCES@
+
+@DISCLAIMER@
+      ]]></help>
+  <expand macro="citations"/>
+</tool>