diff abstracts_by_pmids.xml @ 0:d7aea8ba1e30 draft

"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abstracts_by_pmids.xml	Thu Sep 24 03:11:08 2020 +0000
@@ -0,0 +1,42 @@
+<tool id="abstracts_by_pmids" name="abstracts_by_pmids" version="@VERSION@">
+    <description>For all PMIDs in each row of a table save the according abstracts in additional columns</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>    <expand macro="requirements">
+      <requirement type="package" version="2.0.1">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>
+    </expand>
+    <expand macro="stdio"/>
+    <command><![CDATA[Rscript 
+      '${__tool_directory__}/abstracts_by_pmids.R'
+      --input '$input'
+      --output '$output'
+      ]]>
+    </command>
+    <inputs>
+      <param argument="--input" label="Input file" name="input" optional="false" type="data" format="tabular" help="input"/>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="output" />
+    </outputs>
+    <tests>
+        <test>
+          <param name="input" value="pubmed_by_queries_output" ftype="tabular"/>
+          <output name="output" value="abstracts_by_pmids_output"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns.
+
+Input: 
+able 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.).
+
+Output: 
+A table with additional columns containing abstract texts.
+
+        ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file