# HG changeset patch
# User mingchen0919
# Date 1541795101 18000
# Node ID e0828838e0f3191e4433de163356e46fd78d45c8
# Parent  b8c76b06d7249be5b43ae376123b78d664a8b14a
update

diff -r b8c76b06d724 -r e0828838e0f3 galaxy_outputs.sh
--- a/galaxy_outputs.sh	Fri Nov 09 13:29:21 2018 -0500
+++ b/galaxy_outputs.sh	Fri Nov 09 15:25:01 2018 -0500
@@ -10,6 +10,6 @@
   cp index.html ${REPORT}
 fi
 
-if [ -e "dustmasker_out" ]; then
-  cp dustmasker_out $X_H
+if [ -e "masked_file.txt" ]; then
+  cp masked_file.txt $X_H
 fi
diff -r b8c76b06d724 -r e0828838e0f3 rmarkdown_report.Rmd
--- a/rmarkdown_report.Rmd	Fri Nov 09 13:29:21 2018 -0500
+++ b/rmarkdown_report.Rmd	Fri Nov 09 15:25:01 2018 -0500
@@ -1,5 +1,5 @@
 ---
-title: 'Aurora Tool Report'
+title: 'Dustmasker Report'
 output:
     html_document:
       highlight: pygments
@@ -54,23 +54,21 @@
 ---
 
 
-## Run `dustmasker`
+## Run `dustmasker` job
 
-```{bash}
-dustmasker \
-  -in $X_A \
-  -window $X_B \
-  -level $X_C \
-  -linker $X_D \
-  -infmt $X_E \
-  -outfmt $X_F \
-  
-  $(if [ "$X_G" = "NO_ARGUMENT_YES"  ]; then echo '-parse_seqids'; fi) \
-  
-  -out dustmasker_out
+```{bash echo=FALSE}
+sh ${TOOL_INSTALL_DIR}/scripts_generator.sh
 ```
 
-Options explanation:
+```{r echo=FALSE,warning=FALSE,results='asis'}
+# display content of the job-script.sh file.
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/dustmasker.sh')), sep = '\n')
+cat('\n```')
+```
+
+
+**Options explanation:**
 
 <pre>
 -in <File_In>
@@ -98,5 +96,4 @@
    
  -out <File_Out>
    output file name
-   Default = `-'
 </pre>
\ No newline at end of file
diff -r b8c76b06d724 -r e0828838e0f3 rmarkdown_report.xml
--- a/rmarkdown_report.xml	Fri Nov 09 13:29:21 2018 -0500
+++ b/rmarkdown_report.xml	Fri Nov 09 15:25:01 2018 -0500
@@ -23,20 +23,21 @@
             -d $report.files_path
 
             -A $input_fasta
-            -B $level
-            -C $linker
-            -D $input_format
-            -E $output_format
-            -F $parse_seqids
+            -B $window_length
+            -C $level
+            -D $linker
+            -E $input_format
+            -F $output_format
+            -G $parse_seqids
 
-            -G $out
+            -H $out
 
 
 ]]></command>
   <inputs>
-    <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="input_format_fasta" selected="true">fasta</option><option value="input_format_blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="output_acclist" selected="false">acclist</option><option value="output_fasta" selected="false">fasta</option><option value="output_interval" selected="false">interval</option><option value="output_maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="output_maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="output_maskinfo_xml" selected="false">maskinfo_xml</option><option value="output_seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="output_seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="output_seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs>
+    <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="fasta" selected="true">fasta</option><option value="blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="acclist" selected="false">acclist</option><option value="fasta" selected="true">fasta</option><option value="interval" selected="false">interval</option><option value="maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="maskinfo_xml" selected="false">maskinfo_xml</option><option value="seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs>
   <outputs>
-        <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" label="${tool.name} on ${on_string}" hidden="false"/></outputs>
+        <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" format="fasta" label="${tool.name} on ${on_string}" hidden="false"/></outputs>
   <citations>
         <citation type="bibtex"><![CDATA[
             @article{allaire2016rmarkdown,
diff -r b8c76b06d724 -r e0828838e0f3 scripts_generator.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts_generator.sh	Fri Nov 09 15:25:01 2018 -0500
@@ -0,0 +1,23 @@
+# run SHELL_SCRIPT within tool outputs directory
+cd ${REPORT_FILES_PATH}
+
+
+# generate dustmasker.sh script
+cat >temp.sh <<EOF
+dustmasker \\
+  -in ${X_A} \\
+  -window ${X_B} \\
+  -level ${X_C} \\
+  -linker ${X_D} \\
+  -infmt ${X_E} \\
+  -outfmt ${X_F} \\
+  -parse_seqids ${X_G} \\
+  -out masked_file.txt > dustmasker.log.txt 2>&1
+
+EOF
+
+grep -v 'NO_ARGUMENT_NO' temp.sh > dustmasker.sh
+rm temp.sh
+
+# run dustmasker job
+sh dustmasker.sh
\ No newline at end of file