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+++ b/pubmed_by_queries.xml	Wed Mar 24 08:34:22 2021 +0000
@@ -0,0 +1,85 @@
+<tool id="pubmed_by_queries" name="PubMed query" version="@VERSION@" license="MIT">
+    <description>download a defined number of abstracts or PMIDs from PubMed</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="2.0.3">r-argparse</requirement>
+        <requirement type="package" version="2.13">r-easypubmed</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+    Rscript 
+      '${__tool_directory__}/pubmed_by_queries.R'
+      --input '$input'
+      --output '$output'
+      --number '$number'
+      $abstract
+      #if $__user__.extra_preferences.get('ncbi_account|apikey', ""):
+        -k '$credentials'
+      #end if  
+      ]]>
+    </command>
+
+    <configfiles>
+        <configfile name="credentials"><![CDATA[
+        $__user__.extra_preferences.get('ncbi_account|apikey', "")
+        ]]></configfile>
+    </configfiles>
+
+    <inputs>
+        <param argument="--input" type="data" format="tabular" label="Input file with query terms" />
+        <param argument="--abstract" type="boolean" truevalue="--abstract" falsevalue="" checked="false" label="Save abstracts instead of PMIDs"/>
+        <param argument="--number" type="integer" value="5" min="1" label="Number of PMIDs (or abstracts) to save per ID" />
+    </inputs>
+    
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input" value="test_data" ftype="tabular"/>
+            <param name="number" value="5"/>
+            <param name="abstract" value=""/>
+            <output name="output">
+                <assert_contents>
+                    <has_n_columns n="7"/>
+                    <has_n_lines n="7"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+This tool uses a set of search queries to download a defined number of abstracts or PMIDs for each search query from PubMed.
+PubMed's search rules and syntax apply.
+
+**Info**
+
+To speed up the the download of PubMed data users can obtain an API key from the Settings page of their NCBI account (to create an account, visit http://www.ncbi.nlm.nih.gov/account/) and add it to the Galaxy user-preferences (User/ Preferences/ Manage Information).
+
+-----
+
+**Example**
+
+- Input table:
+    Table with a list of search queries (biomedical entities of interest) in one column. The column header should start with
+    "ID\_" (e.g., "ID_gene" if search queries are genes).
+
+    | ID_gene
+    | 33565071
+    | 33377604
+
+- Output table:
+    Table with additional columns containing PMIDs or abstracts from PubMed (here: PMIDs)
+
+    | ID_gene   | PMID_1        |  PMID_2       |  PMID_3
+    | SCN1A       | 33531663  | 33528079  | 33565071
+    | SCN9A       | 33334860  | 33277917  | 33377604
+
+        ]]></help>
+    <expand macro="citations"/>
+</tool>
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