Mercurial > repos > mingchen0919 > tripal_db_explorer

<tool id="search_contents" name="tripal_db_explorer: search" version="1.0.0">
  <description>&#xD;
    </description>
  <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="1.5">r-jsonlite</requirement><requirement type="package" version="0.2">r-dt</requirement><requirement type="package" version="3.1">r-curl</requirement><requirement type="package" version="1.95_4.8">r-rcurl</requirement></requirements>
  <stdio>
        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
  <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&

Rscript '${__tool_directory__}/'search_contents_render.R

	-o '$report'
	-d '$report.files_path'
	-u '$content_type_url'

	#set $sep = ''
	#set $search_paths = ''
	#for $search_path in $search_section.search_field_repeat:
	  #set $search_paths += $sep + str($search_path.field_path) + ';' + str($search_path.search_operator)
	  #set $sep = '|'
	#end for
	-s '$search_paths'

	#set $sep = ''
	#set $extract_paths = ''
	#for $extract_path in $extract_section.extract_field_repeat:
	  #set $extract_paths += $sep + str($extract_path.field_path)
	  #set $sep = '|'
	#end for
	-e '$extract_paths'

	-l '$records_number'
	-r '$search_results'
]]></command>
  <inputs>
        <param type="text" name="content_type_url" label="Content type URL" optional="False"/><section name="search_section" title="Search: fields" expanded="True"><repeat name="search_field_repeat" title="Field paths" min="1" max="20" default="1"><param type="text" name="field_path" optional="False"/><param type="select" name="search_operator" optional="False"><option value="eq" selected="false">equal (string value)</option><option value="contains" selected="true">contains (string value)</option></param></repeat></section><section name="extract_section" title="Extract: fields" expanded="True"><repeat name="extract_field_repeat" title="Field paths" min="1" max="20" default="1"><param type="text" name="field_path" optional="False"/></repeat></section><param type="integer" name="records_number" label="Records number" help="The maximum number of records to be extracted" optional="False" value="25" min="0"/></inputs>
  <outputs>
        <data name="report" format="html" label="${tool.name} report" hidden="false"/><data name="sink_message" format="txt" label="${tool.name} log" from_work_dir="warnings_and_errors.txt" hidden="false"/><data name="search_results" format="txt" label="${tool.name} results" hidden="false"/></outputs>
  <citations>
        <citation type="bibtex"><![CDATA[
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},
            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
            journal={R package version 0.9},
            volume={6},
            year={2016}
            }
        ]]></citation><citation type="bibtex"><![CDATA[
            @book{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        ]]></citation></citations>
</tool>
author	mingchen0919
date	Mon, 19 Mar 2018 22:44:25 -0400
parents	dbe86b15ee8b
children