changeset 6:8d8cba81fc6e draft

Uploaded

--- a/ideas_genome_tracks.xml	Thu Nov 16 09:04:48 2017 -0500
+++ b/ideas_genome_tracks.xml	Thu Nov 16 09:04:54 2017 -0500
@@ -7,11 +7,9 @@
          <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-#import os
-#set cwd = $os.getcwd()
 #set dbkey = None
-#set input_dir_para = $os.path.abspath($os.path.join($cwd, 'input_dir_para'))
-#set input_dir_state = $os.path.abspath($os.path.join($cwd, 'input_dir_state'))
+#set input_dir_para = "input_dir_para"
+#set input_dir_state = "input_dir_state"
 mkdir $input_dir_para &&
 mkdir $input_dir_state &&
 #for $i in $input:
@@ -23,13 +21,12 @@
     #if $name.endswith(".para"):
         ln -s $filename $input_dir_para/$name &&
     #else if $name.endswith(".state"):
-        n -s $filename $input_dir_state/$name &&
+        ln -s $filename $input_dir_state/$name &&
     #end if
 #end for
 Rscript '$__tool_directory__/ideas_genome_tracks.R'
 -b $dbkey
 -c '$chromInfo'
--d '$track_header'
 -f test
 -p '$input_dir_para'
 -q '$input_dir_state'
@@ -39,7 +36,6 @@
     ]]></command>
     <inputs>
         <param name="input" format="txt" type="data_collection" collection_type="list" label="IDEAS files" />
-        <param name="track_header" type="text" value="" label="Track header"/>
     </inputs>
     <outputs>
         <data name="output_track_db" format="bigbed" label="${tool.name} (track db) on ${on_string}"/>