Mercurial > repos > mingchen0919 > tripal_db_explorer

changeset 8:faddfcea253d draft

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add es_gene_search
author mingchen0919
date Mon, 19 Mar 2018 17:41:50 -0400
parents 7fd14296e7e0
children dbe86b15ee8b
files es_gene_search.xml get_content_types.xml search_contents.xml
diffstat 3 files changed, 103 insertions(+), 44 deletions(-) [+]
line wrap: on
line diff
--- a/es_gene_search.xml	Mon Mar 19 17:32:36 2018 -0400
+++ b/es_gene_search.xml	Mon Mar 19 17:41:50 2018 -0400
@@ -1,10 +1,18 @@
-<tool id="es_gene_search" name="tripal_db_explorer: elasticsearch" version="1.0.0">
-  <description>gene search     </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></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='${__tool_directory__}' &&
+<tool id="es_gene_search" name="tripal_db_explorer: elasticsearch gene search" version="1.0.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+        <requirement type="package" version="1.5">r-jsonlite</requirement>
+        <requirement type="package" version="0.2">r-dt</requirement>
+        <requirement type="package" version="3.1">r-curl</requirement>
+    </requirements>
+    <stdio>
+        <regex match="XXX" source="stderr" level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
+    </stdio>
+    <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
 
 Rscript '${__tool_directory__}/'es_gene_search_render.R
 
@@ -13,11 +21,17 @@
 	-O '$organism'
 	-R '$fasta_results'
 ]]></command>
-  <inputs>
-        <param type="text" name="organism" label="Organism" optional="False"/><param type="text" name="search_keywords" label="Search keywords" optional="False"/></inputs>
-  <outputs>
-        <data format="html" name="report" label="tool report"/><data name="sink_message" format="txt" label="${tool.name} log" from_work_dir="warnings_and_errors.txt" hidden="false"/><data name="fasta_results" format="fasta" label="${tool.name} results" hidden="false"/></outputs>
-  <citations>
+    <inputs>
+        <param type="text" name="organism" label="Organism" optional="False"/>
+        <param type="text" name="search_keywords" label="Search keywords" optional="False"/>
+    </inputs>
+    <outputs>
+        <data format="html" name="report" label="tool report"/>
+        <data name="sink_message" format="txt" label="${tool.name} log" from_work_dir="warnings_and_errors.txt"
+              hidden="false"/>
+        <data name="fasta_results" format="fasta" label="${tool.name} results" hidden="false"/>
+    </outputs>
+    <citations>
         <citation type="bibtex"><![CDATA[
             @article{allaire2016rmarkdown,
             title={rmarkdown: Dynamic Documents for R, 2016},
@@ -27,7 +41,8 @@
             volume={6},
             year={2016}
             }
-        ]]></citation><citation type="bibtex"><![CDATA[
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[
             @book{xie2015dynamic,
             title={Dynamic Documents with R and knitr},
             author={Xie, Yihui},
@@ -35,5 +50,6 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation></citations>
+        ]]></citation>
+    </citations>
 </tool>
--- a/get_content_types.xml	Mon Mar 19 17:32:36 2018 -0400
+++ b/get_content_types.xml	Mon Mar 19 17:41:50 2018 -0400
@@ -1,11 +1,18 @@
-<tool id="get_content_types" name="Get content types" version="1.0.0">
-  <description>Tripal database explorer: get content types&#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></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='${__tool_directory__}' &&
+<tool id="get_content_types" name="tripal_db_explorer: resources summary" version="1.0.0">
+    <description/>
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+        <requirement type="package" version="1.5">r-jsonlite</requirement>
+        <requirement type="package" version="0.2">r-dt</requirement>
+        <requirement type="package" version="3.1">r-curl</requirement>
+    </requirements>
+    <stdio>
+        <regex match="XXX" source="stderr" level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
+    </stdio>
+    <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
 
 Rscript '${__tool_directory__}/'get_content_types_render.R
 
@@ -14,11 +21,15 @@
 	-s '$sink_message'
 	-u '$web_services_root_url'
 ]]></command>
-  <inputs>
-        <param type="text" name="web_services_root_url" label="Web services root URL" optional="False"/></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"/></outputs>
-  <citations>
+    <inputs>
+        <param type="text" name="web_services_root_url" label="Web services root URL" optional="False"/>
+    </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"/>
+    </outputs>
+    <citations>
         <citation type="bibtex"><![CDATA[
             @article{allaire2016rmarkdown,
             title={rmarkdown: Dynamic Documents for R, 2016},
@@ -28,7 +39,8 @@
             volume={6},
             year={2016}
             }
-        ]]></citation><citation type="bibtex"><![CDATA[
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[
             @book{xie2015dynamic,
             title={Dynamic Documents with R and knitr},
             author={Xie, Yihui},
@@ -36,5 +48,6 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation></citations>
+        ]]></citation>
+    </citations>
 </tool>
--- a/search_contents.xml	Mon Mar 19 17:32:36 2018 -0400
+++ b/search_contents.xml	Mon Mar 19 17:41:50 2018 -0400
@@ -1,12 +1,19 @@
-<tool id="search_contents" name="Search contents" version="1.0.0">
-  <description>
-        some description
+<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></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='${__tool_directory__}' &&
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+        <requirement type="package" version="1.5">r-jsonlite</requirement>
+        <requirement type="package" version="0.2">r-dt</requirement>
+        <requirement type="package" version="3.1">r-curl</requirement>
+    </requirements>
+    <stdio>
+        <regex match="XXX" source="stderr" level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
+    </stdio>
+    <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
 
 Rscript '${__tool_directory__}/'search_contents_render.R
 
@@ -33,11 +40,32 @@
 	-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="${tool.name} results" hidden="false"/></outputs>
-  <citations>
+    <inputs>
+        <param type="text" name="content_type_url" label="Content type URL" optional="False"/>
+        <section name="search_section" title="Search: fields" expanded="True">
+            <repeat name="search_field_repeat" title="Field paths" min="1" max="20" default="1">
+                <param type="text" name="field_path" optional="False"/>
+                <param type="select" name="search_operator" optional="False">
+                    <option value="eq" selected="false">equal (string value)</option>
+                    <option value="contains" selected="true">contains (string value)</option>
+                </param>
+            </repeat>
+        </section>
+        <section name="extract_section" title="Extract: fields" expanded="True">
+            <repeat name="extract_field_repeat" title="Field paths" min="1" max="20" default="1">
+                <param type="text" name="field_path" optional="False"/>
+            </repeat>
+        </section>
+        <param type="integer" name="records_number" label="Records number"
+               help="The maximum number of records to be extracted" optional="False" value="25" min="0"/>
+    </inputs>
+    <outputs>
+        <data name="report" format="html" label="${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},
@@ -47,7 +75,8 @@
             volume={6},
             year={2016}
             }
-        ]]></citation><citation type="bibtex"><![CDATA[
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[
             @book{xie2015dynamic,
             title={Dynamic Documents with R and knitr},
             author={Xie, Yihui},
@@ -55,5 +84,6 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation></citations>
+        ]]></citation>
+    </citations>
 </tool>