# HG changeset patch
# User mingchen0919
# Date 1526387200 14400
# Node ID 3d4f21a85f68fbf236e456876126108cef420046
# Parent  dfd29c07d6ca330e6d23161b0702a7fc5d839318
planemo upload

diff -r dfd29c07d6ca -r 3d4f21a85f68 build-and-run-job-scripts.sh
--- a/build-and-run-job-scripts.sh	Tue May 15 00:52:51 2018 -0400
+++ b/build-and-run-job-scripts.sh	Tue May 15 08:26:40 2018 -0400
@@ -3,11 +3,10 @@
 
 #========== build and run job 1 script ============
 cat >curl-download.sh <<EOF
-if [ "$X_f" != 'None' ];then
+if [[ $(wc -l <$X_f) -ge 2 ]];then
   cp $X_f $X_O
-elif [ "$X_u" != "TRUE" ];then
-  curl $X_u > $X_O
-fi
+else
+  curl $(head -1 $X_f) > $X_O
 EOF
 
 # run job 1 script
diff -r dfd29c07d6ca -r 3d4f21a85f68 command-line-arguments.csv
--- a/command-line-arguments.csv	Tue May 15 00:52:51 2018 -0400
+++ b/command-line-arguments.csv	Tue May 15 08:26:40 2018 -0400
@@ -2,6 +2,5 @@
 o,1,character,report
 d,1,character,report.files_path
 f,1,character,upload_fasta
-u,2,character,url_fasta
 O,1,character,output_fasta
 
diff -r dfd29c07d6ca -r 3d4f21a85f68 rmarkdown_report.xml
--- a/rmarkdown_report.xml	Tue May 15 00:52:51 2018 -0400
+++ b/rmarkdown_report.xml	Tue May 15 08:26:40 2018 -0400
@@ -30,19 +30,17 @@
             -d $report.files_path
             
             -f $upload_fasta
-            -u $url_fasta
             -O $output_fasta
 
 
     ]]></command>
     <inputs>
-        <param type="data" name="upload_fasta" format="fa,fna,fasta" label="Fasta file from history"
-               optional="True"/>
-        <param type="text" name="url_fasta" label="URL to downloadable fasta file"/>
+        <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."/>
     </inputs>
     <outputs>
-        <data format="html" name="report" label="${tool.name} report on ${on_string}" />
-        <data format="fasta" name="output_fasta" label="${tool.name} fasta on ${on_string}" />
+        <data format="html" name="report" label="${tool.name} report on ${on_string}"/>
+        <data format="fasta" name="output_fasta" label="${tool.name} fasta"/>
     </outputs>
     <citations>
         <citation type="bibtex"><![CDATA[