# HG changeset patch
# User mingchen0919
# Date 1526485910 14400
# Node ID 63e9ce43c1eedd802919106d465d8c2bf5cfe2d3
# Parent  8850e8e60977e119f36bea39d6831e0f16cf1863
planemo upload

diff -r 8850e8e60977 -r 63e9ce43c1ee build-and-run-job-scripts.sh
--- a/build-and-run-job-scripts.sh	Tue May 15 09:00:22 2018 -0400
+++ b/build-and-run-job-scripts.sh	Wed May 16 11:51:50 2018 -0400
@@ -3,10 +3,22 @@
 
 #========== build and run job 1 script ============
 cat >curl-download.sh <<EOF
-# use the first line as an url and start downloading. If it failed, run the second command.
-curl $(head -1 $X_f) > $X_O || cp $X_f $X_O
+if [ $(wc -l <$X_f) -gt 2 ]; then
+  cp $X_f $X_O
+else
+  if [ "$X_e" = "twobit" ]; then
+    cp $TOOL_INSTALL_DIR/twoBitToFa twoBitToFa
+    chmod +x twoBitToFa
+    ./twoBitToFa $(head -1 $X_f) $X_O
+  elif [ "$X_e" = "gz" ]; then
+    curl $(head -1 $X_f) > output.fa.gz 
+    gunzip -c output.fa.gz > $X_O 
+  else
+    curl $(head -1 $X_f) > $X_O
+  fi
+fi
+
 EOF
 
-# run job 1 script
 sh curl-download.sh
 
diff -r 8850e8e60977 -r 63e9ce43c1ee command-line-arguments.csv
--- a/command-line-arguments.csv	Tue May 15 09:00:22 2018 -0400
+++ b/command-line-arguments.csv	Wed May 16 11:51:50 2018 -0400
@@ -2,5 +2,6 @@
 o,1,character,report
 d,1,character,report.files_path
 f,1,character,upload_fasta
+e,1,character,url_ext
 O,1,character,output_fasta
 
diff -r 8850e8e60977 -r 63e9ce43c1ee rmarkdown_report.xml
--- a/rmarkdown_report.xml	Tue May 15 09:00:22 2018 -0400
+++ b/rmarkdown_report.xml	Wed May 16 11:51:50 2018 -0400
@@ -30,6 +30,7 @@
             -d $report.files_path
             
             -f $upload_fasta
+            -e $url_ext
             -O $output_fasta
 
 
@@ -37,6 +38,11 @@
     <inputs>
         <param type="data" name="upload_fasta" format="txt,fa,fna,fasta" label="Fasta file or Fasta URL"
                help="A fasta file or a txt file. If it is txt file, it should only has one line, which is an URL to a downloadable fasta file."/>
+        <param type="select" name="url_ext" label="URL fasta format">
+            <option value="fasta" selected="true">.fa, .fasta</option>
+            <option value="gz">.gz</option>
+            <option value="twobit">.2bit</option>
+        </param>
     </inputs>
     <outputs>
         <data format="html" name="report" label="${tool.name} report on ${on_string}"/>
diff -r 8850e8e60977 -r 63e9ce43c1ee twoBitToFa
Binary file twoBitToFa has changed