diff ideas_genome_tracks.xml @ 66:f0c488b73dbc draft

Uploaded

--- a/ideas_genome_tracks.xml	Tue Dec 19 12:53:24 2017 -0500
+++ b/ideas_genome_tracks.xml	Wed Dec 20 11:26:04 2017 -0500
@@ -4,7 +4,6 @@
         <requirement type="package" version="2.4.27">bedops</requirement>
         <requirement type="package" version="1.10.4">r-data.table</requirement>
          <requirement type="package" version="1.4.4">r-optparse</requirement>
-         <requirement type="package" version="0.2.0">r-viridislite</requirement>
          <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
@@ -19,6 +18,7 @@
 #else:
     #set email = $__user__.email
 #end if
+#set input_dir_state = "input_dir_para"
 #set input_dir_state = "input_dir_state"
 #set select_state_color = $select_state_color_cond.select_state_color
 #if str($select_state_color) == 'yes':
@@ -32,6 +32,7 @@
     #set state_indexes = ",".join($state_indexes)
     #set state_colors = ",".join($state_colors)
 #end if
+mkdir $input_dir_para &&
 mkdir $input_dir_state &&
 mkdir '$output_trackhub.files_path' &&
 #for $i in $input:
@@ -40,7 +41,9 @@
     #end if
     #set filename = $i.file_name
     #set name = $i.name
-    #if $name.endswith(".state"):
+    #if $name.endswith(".para"):
+        ln -s $filename $input_dir_para/$name &&
+    #else if $name.endswith(".state"):
         ln -s $filename $input_dir_state/$name &&
     #end if
 #end for
@@ -50,6 +53,7 @@
 --email '$email'
 --galaxy_url $galaxy_url
 --hub_name '$hub_name'
+--input_dir_para '$input_dir_para'
 --input_dir_state '$input_dir_state'
 --long_label '$sanitized_long_label'
 --output_trackhub '$output_trackhub'
@@ -76,7 +80,7 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <repeat name="state_color_repeat" title="State colors" min="1">
+                <repeat name="state_color_repeat" title="state color" min="1">
                     <param name="state_index" type="integer" value="" min="1" label="State index" help="Enter the integer index of the desired state">
                         <validator type="empty_field"/>
                     </param>