Mercurial > repos > mingchen0919 > tripal_db_explorer

changeset 9:dbe86b15ee8b draft

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add r-rcurl
author mingchen0919
date Mon, 19 Mar 2018 22:30:54 -0400
parents faddfcea253d
children c67d7ad8ac02
files es_gene_search.Rmd es_gene_search.csv es_gene_search.sh es_gene_search.xml get_content_types.xml search_contents.xml
diffstat 6 files changed, 50 insertions(+), 101 deletions(-) [+]
line wrap: on
line diff
--- a/es_gene_search.Rmd	Mon Mar 19 17:41:50 2018 -0400
+++ b/es_gene_search.Rmd	Mon Mar 19 22:30:54 2018 -0400
@@ -21,7 +21,11 @@
 ```
 
 ```{r 'ste[ 2'}
-
+download_url = paste0(opt$X_U, '/elasticsearch/gene_download?',
+             'organism=', RCurl::curlEscape(opt$X_O), '&',
+             'search_term=', RCurl::curlEscape(opt$X_K))
+print(download_url)
+download.file(download_url, destfile = opt$X_R)
 ```
 
 
--- a/es_gene_search.csv	Mon Mar 19 17:41:50 2018 -0400
+++ b/es_gene_search.csv	Mon Mar 19 22:30:54 2018 -0400
@@ -1,5 +1,7 @@
 short flag,argument mask,data type,variable name,galaxy input type,description
 o,1,character,report,data,
 d,1,character,report.files_path,data,
+U,1,character,tripal_db_url,text,
 O,1,character,organism,text,
+K,1,character,search_keywords,text,
 R,1,character,fasta_results,text,
--- a/es_gene_search.sh	Mon Mar 19 17:41:50 2018 -0400
+++ b/es_gene_search.sh	Mon Mar 19 22:30:54 2018 -0400
@@ -4,5 +4,7 @@
 
 	-o '$report'
 	-d '$report.files_path'
+	-U '$tripal_db_url'
 	-O '$organism'
+	-K '$search_keywords'
 	-R '$fasta_results'
--- a/es_gene_search.xml	Mon Mar 19 17:41:50 2018 -0400
+++ b/es_gene_search.xml	Mon Mar 19 22:30:54 2018 -0400
@@ -1,37 +1,25 @@
 <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='${__tool_directory__}' &&
+  <description>  </description>
+  <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="1.5">r-jsonlite</requirement><requirement type="package" version="0.2">r-dt</requirement><requirement type="package" version="3.1">r-curl</requirement><requirement type="package" version="1.95_4.9">r-rcurl</requirement></requirements>
+  <stdio>
+        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
+  <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
 
 Rscript '${__tool_directory__}/'es_gene_search_render.R
 
 	-o '$report'
 	-d '$report.files_path'
+	-U '$tripal_db_url'
 	-O '$organism'
+	-K '$search_keywords'
 	-R '$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="tripal_db_url" label="Tripal database URL" optional="False"/><param type="text" name="organism" label="Organism" optional="False"/><param type="text" name="search_keywords" label="Search keywords" optional="False"/><param type="boolean" name="download_fasta" label="Save gene sequences to fasta file" optional="False" truevalue="TRUE" falsevalue="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"/><data name="fasta_results" format="fasta" label="${tool.name} results" hidden="false"/></outputs>
+  <citations>
         <citation type="bibtex"><![CDATA[
             @article{allaire2016rmarkdown,
             title={rmarkdown: Dynamic Documents for R, 2016},
@@ -41,8 +29,7 @@
             volume={6},
             year={2016}
             }
-        ]]></citation>
-        <citation type="bibtex"><![CDATA[
+        ]]></citation><citation type="bibtex"><![CDATA[
             @book{xie2015dynamic,
             title={Dynamic Documents with R and knitr},
             author={Xie, Yihui},
@@ -50,6 +37,5 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation>
-    </citations>
+        ]]></citation></citations>
 </tool>
--- a/get_content_types.xml	Mon Mar 19 17:41:50 2018 -0400
+++ b/get_content_types.xml	Mon Mar 19 22:30:54 2018 -0400
@@ -1,18 +1,10 @@
 <tool id="get_content_types" name="tripal_db_explorer: resources summary" version="1.0.0">
-    <description/>
-    <requirements>
-        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
-        <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="1.6">r-rmarkdown</requirement>
-        <requirement type="package" version="1.5">r-jsonlite</requirement>
-        <requirement type="package" version="0.2">r-dt</requirement>
-        <requirement type="package" version="3.1">r-curl</requirement>
-    </requirements>
-    <stdio>
-        <regex match="XXX" source="stderr" level="warning"
-               description="Check the warnings_and_errors.txt file for more details."/>
-    </stdio>
-    <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
+  <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_4.9">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__}/'get_content_types_render.R
 
@@ -21,15 +13,11 @@
 	-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},
@@ -39,8 +27,7 @@
             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},
@@ -48,6 +35,5 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation>
-    </citations>
+        ]]></citation></citations>
 </tool>
--- a/search_contents.xml	Mon Mar 19 17:41:50 2018 -0400
+++ b/search_contents.xml	Mon Mar 19 22:30:54 2018 -0400
@@ -1,19 +1,11 @@
 <tool id="search_contents" name="tripal_db_explorer: search" version="1.0.0">
-    <description>&#xD;
+  <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='${__tool_directory__}' &&
+  <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="1.5">r-jsonlite</requirement><requirement type="package" version="0.2">r-dt</requirement><requirement type="package" version="3.1">r-curl</requirement><requirement type="package" version="1.95_4.9">r-rcurl</requirement></requirements>
+  <stdio>
+        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
+  <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
 
 Rscript '${__tool_directory__}/'search_contents_render.R
 
@@ -40,32 +32,11 @@
 	-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},
@@ -75,8 +46,7 @@
             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},
@@ -84,6 +54,5 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation>
-    </citations>
+        ]]></citation></citations>
 </tool>