changeset 7:7fd14296e7e0 draft

add es_gene_search
author mingchen0919
date Mon, 19 Mar 2018 17:32:36 -0400
parents 4bc7752bfd72
children faddfcea253d
files es_gene_search.Rmd es_gene_search.csv es_gene_search.sh es_gene_search.xml es_gene_search_render.R get_content_types.xml search_contents.xml
diffstat 7 files changed, 158 insertions(+), 73 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/es_gene_search.Rmd	Mon Mar 19 17:32:36 2018 -0400
@@ -0,0 +1,27 @@
+---
+title: 'HTML report title'
+output:
+    html_document:
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = TRUE,
+  error = TRUE
+)
+```
+
+
+# Code for computational analysis
+
+```{r 'step 1'}
+opt
+```
+
+```{r 'ste[ 2'}
+
+```
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/es_gene_search.csv	Mon Mar 19 17:32:36 2018 -0400
@@ -0,0 +1,5 @@
+short flag,argument mask,data type,variable name,galaxy input type,description
+o,1,character,report,data,
+d,1,character,report.files_path,data,
+O,1,character,organism,text,
+R,1,character,fasta_results,text,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/es_gene_search.sh	Mon Mar 19 17:32:36 2018 -0400
@@ -0,0 +1,8 @@
+export TOOL_DIR='${__tool_directory__}' &&
+
+Rscript '${__tool_directory__}/'es_gene_search_render.R
+
+	-o '$report'
+	-d '$report.files_path'
+	-O '$organism'
+	-R '$fasta_results'
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/es_gene_search.xml	Mon Mar 19 17:32:36 2018 -0400
@@ -0,0 +1,39 @@
+<tool id="es_gene_search" name="tripal_db_explorer: elasticsearch" version="1.0.0">
+  <description>gene search     </description>
+  <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="1.5">r-jsonlite</requirement><requirement type="package" version="0.2">r-dt</requirement><requirement type="package" version="3.1">r-curl</requirement></requirements>
+  <stdio>
+        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
+  <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
+
+Rscript '${__tool_directory__}/'es_gene_search_render.R
+
+	-o '$report'
+	-d '$report.files_path'
+	-O '$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="${tool.name} results" hidden="false"/></outputs>
+  <citations>
+        <citation type="bibtex"><![CDATA[
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        ]]></citation><citation type="bibtex"><![CDATA[
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        ]]></citation></citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/es_gene_search_render.R	Mon Mar 19 17:32:36 2018 -0400
@@ -0,0 +1,50 @@
+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file('warnings_and_errors.txt')
+sink(zz)
+sink(zz, type = 'message')
+
+#------------import libraries--------------------
+options(stringsAsFactors = FALSE)
+
+library(getopt)
+library(rmarkdown)
+#------------------------------------------------
+
+
+#------------get arguments into R--------------------
+# load helper function
+source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R'))
+# import getopt specification matrix from a csv file
+opt = getopt(getopt_specification_matrix('/es_gene_search.csv'))
+opt$X_t = Sys.getenv('TOOL_DIR')
+#----------------------------------------------------
+
+
+#-----------using passed arguments in R
+#           to define system environment variables---
+do.call(Sys.setenv, opt[-1])
+#----------------------------------------------------
+
+#---------- often used variables ----------------
+# OUTPUT_DIR: path to the output associated directory, which stores all outputs
+# TOOL_DIR: path to the tool installation directory
+OUTPUT_DIR = opt$X_d
+TOOL_DIR =   opt$X_t
+OUTPUT_REPORT = opt$X_o
+RMD_NAME = 'es_gene_search.Rmd'
+
+# create the output associated directory to store all outputs
+dir.create(OUTPUT_DIR, recursive = TRUE)
+
+#-----------------render Rmd--------------
+render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
+#------------------------------------------
+
+#==============the end==============
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
--- a/get_content_types.xml	Mon Mar 19 16:29:51 2018 -0400
+++ b/get_content_types.xml	Mon Mar 19 17:32:36 2018 -0400
@@ -1,19 +1,11 @@
-<tool id="get_content_types" name="tripal_db_explorer: resources summary" version="1.0.0">
-    <description>
+<tool id="get_content_types" name="Get content types" version="1.0.0">
+  <description>Tripal database explorer: get content types&#xD;
     </description>
-    <requirements>
-        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
-        <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="1.6">r-rmarkdown</requirement>
-        <requirement type="package" version="1.5">r-jsonlite</requirement>
-        <requirement type="package" version="0.2">r-dt</requirement>
-        <requirement type="package" version="3.1">r-curl</requirement>
-    </requirements>
-    <stdio>
-        <regex match="XXX" source="stderr" level="warning"
-               description="Check the warnings_and_errors.txt file for more details."/>
-    </stdio>
-    <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
+  <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
 
@@ -22,15 +14,11 @@
 	-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},
@@ -40,8 +28,7 @@
             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},
@@ -49,6 +36,5 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation>
-    </citations>
+        ]]></citation></citations>
 </tool>
--- a/search_contents.xml	Mon Mar 19 16:29:51 2018 -0400
+++ b/search_contents.xml	Mon Mar 19 17:32:36 2018 -0400
@@ -1,19 +1,12 @@
-<tool id="search_contents" name="tripal_db_explorer: search" version="1.0.0">
-    <description>
+<tool id="search_contents" name="Search contents" version="1.0.0">
+  <description>
+        some 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='${__tool_directory__}' &&
+  <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="1.5">r-jsonlite</requirement><requirement type="package" version="0.2">r-dt</requirement><requirement type="package" version="3.1">r-curl</requirement></requirements>
+  <stdio>
+        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
+  <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
 
 Rscript '${__tool_directory__}/'search_contents_render.R
 
@@ -40,32 +33,11 @@
 	-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 +47,7 @@
             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 +55,5 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation>
-    </citations>
+        ]]></citation></citations>
 </tool>