diff pubmed_by_queries.xml @ 0:f40606281050 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/pubmed_by_queries.xml	Thu Sep 24 03:01:43 2020 +0000
@@ -0,0 +1,56 @@
+<tool id="pubmed_by_queries" name="pubmed_by_queries" version="@VERSION@">
+    <description>Download a defined number of abstracts or PMIDs from PubMed for a set of search queries</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+      <requirement type="package" version="2.0.1">r-argparse</requirement>
+      <requirement type="package" version="2.13">r-easypubmed</requirement>
+    </expand>
+    <expand macro="stdio"/>
+    <command><![CDATA[Rscript 
+      '${__tool_directory__}/pubmed_by_queries.R'
+      --input '$input'
+      --output '$output'
+      --number '$number'
+      $abstract
+      #if str($key):
+      --key '$key'
+      #end if
+      ]]>
+    </command>
+    
+    <inputs>
+      <param argument="--input" label="Input file" name="input" optional="false" type="data" format="tabular" help="input"/>
+      <param argument="--abstract" label="Save abstracts instead of PMIDs" name="abstract" type="boolean" truevalue="--abstract" falsevalue="" help="abstract" checked="false"/>
+      <param argument="--number" label="Number of PMIDs (or abstracts) to save per  ID" name="number" optional="false" type="integer" help="number" value="5"/>
+      <param argument="--key" label="NCBI API key (if available)" name="key" optional="true" type="text" help="key"/>
+    </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" value="pubmed_by_queries_output"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+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.
+ 
+Input:
+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).
+
+Output: 
+Table with additional columns containing PMIDs or abstracts from PubMed.
+
+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/).
+
+        ]]></help>
+    <expand macro="citations"/>
+</tool>
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