Mercurial > repos > greg > ideas_genome_tracks

changeset 10:2b484c93d20a draft

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Uploaded
author greg
date Thu, 16 Nov 2017 13:18:58 -0500
parents ecc2397d5aeb
children 45a2f84b8247
files ideas_genome_tracks.xml
diffstat 1 files changed, 10 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_genome_tracks.xml	Thu Nov 16 09:59:45 2017 -0500
+++ b/ideas_genome_tracks.xml	Thu Nov 16 13:18:58 2017 -0500
@@ -8,11 +8,16 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #set dbkey = None
+#if str($__user__.email) == 'None':
+    #set email = "foo@bar.net"
+#else:
+    #set email = $__user__.email
+#end if
 #set input_dir_para = "input_dir_para"
 #set input_dir_state = "input_dir_state"
 mkdir $input_dir_para &&
 mkdir $input_dir_state &&
-mkdir '$output_hub.files_path' &&
+mkdir '$output_trackhub.files_path' &&
 #for $i in $input:
     #if $dbkey is None:
         #set dbkey = $i.metadata.dbkey
@@ -29,20 +34,17 @@
 -b $dbkey
 -c '$chromInfo'
 -f test
+-g '$email'
 -p '$input_dir_para'
 -q '$input_dir_state'
--u '$output_track_db'
--v '$output_build'
--w '$output_hub'
--x '$output_hub.files_path'
+-w '$output_trackhub'
+-x '$output_trackhub.files_path'
     ]]></command>
     <inputs>
         <param name="input" format="txt" type="data_collection" collection_type="list" label="IDEAS files" />
     </inputs>
     <outputs>
-        <data name="output_track_db" format="bigbed" label="${tool.name} (track db) on ${on_string}"/>
-        <data name="output_build" format="txt" label="${tool.name} (genome build) on ${on_string}"/>
-        <data name="output_hub" format="trackhub" label="${tool.name} (track hub) on ${on_string}"/>
+        <data name="output_trackhub" format="trackhub"/>
     </outputs>
     <tests>
         <test>