Mercurial > repos > greg > ideas_genome_tracks

changeset 19:8cd8dabdca19 draft

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Uploaded
author greg
date Mon, 20 Nov 2017 10:34:29 -0500
parents 0bd424ce10fb
children 696e435f5607
files ideas_genome_tracks.xml
diffstat 1 files changed, 15 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_genome_tracks.xml	Thu Nov 16 14:48:23 2017 -0500
+++ b/ideas_genome_tracks.xml	Mon Nov 20 10:34:29 2017 -0500
@@ -7,7 +7,9 @@
          <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+#import string
 #set dbkey = None
+#set sanitized_hub_name = $hub_name.translate(dict.fromkeys(map(ord, whitespace)))
 #if str($__user__.email) == 'None':
     #set email = "foo@bar.net"
 #else:
@@ -33,16 +35,27 @@
 Rscript '$__tool_directory__/ideas_genome_tracks.R'
 -b $dbkey
 -c '$chromInfo'
--f test
--g '$email'
+-e '$email'
+-l '$long_label[:79]'
+-n '$sanitized_hub_name'
 -p '$input_dir_para'
 -q '$input_dir_state'
+-s '$short_label[:16]'
 -w '$output_trackhub'
 -x '$output_trackhub.files_path'
 &>/dev/null
     ]]></command>
     <inputs>
         <param name="input" format="txt" type="data_collection" collection_type="list" label="IDEAS files" />
+        <param name="hub_name" type="text" value="" label="Hub name" help="All white space characters will be eliminated">
+            <validator type="empty_field"/>
+        </param>
+        <param name="short_label" type="text" value="short label" label="Short label" help="Limit to 17 characters">
+            <validator type="empty_field"/>
+        </param>
+        <param name="long_label" type="text" value="long label" label="Long label" help="Limit to 80 characters">
+            <validator type="empty_field"/>
+        </param>
     </inputs>
     <outputs>
         <data name="output_trackhub" format="trackhub"/>