Mercurial > repos > iuc > ncbi_eutils_ecitmatch
diff ecitmatch.xml @ 0:68cd8d564e0a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author | iuc |
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date | Thu, 07 Jul 2016 02:39:21 -0400 |
parents | |
children | 1dff3adb0a97 |
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--- /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>