diff abstracts_by_pmids.xml @ 0:ff904894ccaa draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abstracts_by_pmids.xml	Wed Mar 24 08:32:54 2021 +0000
@@ -0,0 +1,61 @@
+<tool id="abstracts_by_pmids" name="Get PubMed abstracts" version="@VERSION@" license="MIT">
+    <description>by PMID IDs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>    
+    <requirements>
+        <requirement type="package" version="2.0.3">r-argparse</requirement>
+        <requirement type="package" version="0.2.3">r-reutils</requirement>
+        <requirement type="package" version="2.13">r-easypubmed</requirement>
+        <requirement type="package" version="0.9.3">r-textclean</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    Rscript 
+      '${__tool_directory__}/abstracts_by_pmids.R'
+      --input '$input'
+      --output '$output'
+      ]]>
+    </command>
+    <inputs>
+        <param argument="--input" type="data" format="tabular" label="Input file with PMID IDs" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="pubmed_by_queries_output" ftype="tabular"/>
+            <output name="output">
+                <assert_contents>
+                    <has_n_lines n="7"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns.
+
+-----
+
+**Example**
+
+- Input file:
+    Table with rows representing biomedical entities and columns containing the corresponding PMIDs. The names of the PMID columns should start with “PMID\_” (e.g., “PMID_1”, “PMID_2” etc.).
+
+    | PMID_1      | PMID_2      | PMID_2      
+    | 33565071    | 33531663    | 33528079    
+    | 33377604    | 33334860    | 33277917    
+
+- Output file:
+    A table with additional columns containing the abstract texts.
+
+    | PMID_1      | PMID_2      | PMID_2      | ABSTRACT_1  | ABSTRACT_3  | ABSTRACT_3  
+    | 33565071    | 33531663    | 33528079    | abc def...    | abc def...    | abc def...    
+    | 33377604    | 33334860    | 33277917    | abc def...    | abc def...    | abc def...    
+
+        ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file