diff ecitmatch.xml @ 0:68cd8d564e0a 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/ecitmatch.xml	Thu Jul 07 02:39:21 2016 -0400
@@ -0,0 +1,105 @@
+<?xml version="1.0"?>
+<tool id="ncbi_eutils_ecitmatch" name="NCBI ECitMatch" version="@WRAPPER_VERSION@">
+  <description>search NCBI for citations in PubMed</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <version_command>python ecitmatch.py --version</version_command>
+  <command detect_errors="aggressive" interpreter="python"><![CDATA[ecitmatch.py
+
+#if str($input.method) == "file":
+    --file $input.citation_file
+#else
+    #set keys = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
+    #set journal_title = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
+    #set year = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
+    #set volume = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
+    #set first_page = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
+    #set author = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
+
+    --key "$keys"
+    --journal_title "$journal_title"
+    --key "$year"
+    --key "$volume"
+    --key "$first_page"
+    --key "$author"
+#end if
+
+@EMAIL_ARGUMENTS@
+> $default]]></command>
+  <inputs>
+    <conditional name="input">
+      <param name="method" type="select" label="Input method">
+        <option value="file">Load citations from a formatted table</option>
+        <option value="direct">Direct Input</option>
+      </param>
+      <when value="file">
+          <param label="Citation table" name="citation_file" type="data"
+              format="tabular" help="Columns must be in a specific order, see help documentation"/>
+      </when>
+      <when value="direct">
+        <repeat name="citations" title="Citations">
+          <param name="journal_title" type="text" label="Journal Title"
+            help="E.g. proc natl acad sci u s a" />
+          <param name="year" type="integer" label="Year" value="2000"/>
+          <param name="volume" type="integer" label="Volume" value="88"/>
+          <param name="first_page" type="integer" label="First Page" value="1"/>
+          <param name="author" type="text" label="Author's Name" />
+          <param name="key" type="text" label="Citation key"
+            help="Used to match input results to NCBI's output" />
+        </repeat>
+      </when>
+    </conditional>
+
+  </inputs>
+  <outputs>
+    <data format="tabular" name="default" label="ECitMatch Results"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="method" value="file"/>
+      <param name="citation_file" value="ecitmatch.tsv"/>
+      <output name="default" file="ecitmatch.results.tsv" ftype="tabular"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+NCBI ECitMatch
+==============
+
+Search for citation PubMed IDs. These can be provided via a tabular file, or
+via direct input. If provided via file, the columns should be ordered:
+
+1. Journal Name
+2. Year
+3. Volume
+4. First Page
+5. Author Name
+6. Citation Key
+
+
+An example query:
+
++---------------+--------------------------+
+| Parameter     | Value                    |
++===============+==========================+
+| Journal Title | proc natl acad sci u s a |
++---------------+--------------------------+
+| Year          | 1991                     |
++---------------+--------------------------+
+| Volume        | 88                       |
++---------------+--------------------------+
+| First Page    | 3248                     |
++---------------+--------------------------+
+| Author Name   | mann bj                  |
++---------------+--------------------------+
+| Citation Key  | citation_1               |
++---------------+--------------------------+
+
+
+@REFERENCES@
+
+@DISCLAIMER@
+      ]]></help>
+  <expand macro="citations"/>
+</tool>