Mercurial > repos > greg > ideas_genome_tracks

changeset 29:fc6f39767c83 draft

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Uploaded
author greg
date Tue, 21 Nov 2017 13:23:28 -0500
parents bc1e9eb54f3c
children 4c42188478a7
files ideas_genome_tracks.R ideas_genome_tracks.xml test-data/IDEAS_out.cluster test-data/IDEAS_out.para test-data/IDEAS_out.profile test-data/IDEAS_out.state test-data/e001-h3k4me3.bigwig test-data/output_trackhub.html test-data/test.bed
diffstat 9 files changed, 85 insertions(+), 55 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_genome_tracks.R	Tue Nov 21 09:04:59 2017 -0500
+++ b/ideas_genome_tracks.R	Tue Nov 21 13:23:28 2017 -0500
@@ -88,12 +88,12 @@
 
 create_primary_html = function(output_trackhub, tracks_dir) {
     track_files <- list.files(path=tracks_dir);
-    s <- paste('<html>\n<head>\n</head>\n<body>\n<ul>\n', sep="");
+    s <- paste('<html>\n    <head>\n    </head>\n    <body>\n        <ul>\n', sep="");
         for (i in 1:length(track_files)) {
             track_file <- paste("tracks", track_files[i], sep="/");
-            s <- paste(s, '<li>\n<a href="', track_file, '">', track_file, '</a>\n</li>', sep="");
+            s <- paste(s, '            <li><a href="', track_file, '">', track_file, '</a></li>\n', sep="");
         }
-    s <- paste(s, '</ul>\n</body>\n</html>', sep="");
+    s <- paste(s, '        </ul>\n    </body>\n</html>', sep="");
     cat(s, file=output_trackhub);
 }
 
--- a/ideas_genome_tracks.xml	Tue Nov 21 09:04:59 2017 -0500
+++ b/ideas_genome_tracks.xml	Tue Nov 21 13:23:28 2017 -0500
@@ -48,7 +48,7 @@
 #end if
 -w '$output_trackhub'
 -x '$output_trackhub.files_path'
-&>/dev/null
+&>proc.log
     ]]></command>
     <inputs>
         <param name="input" format="txt" type="data_collection" collection_type="list" label="IDEAS files"/>
@@ -62,7 +62,7 @@
             <validator type="empty_field"/>
         </param>
         <conditional name="set_track_color_cond">
-            <param name="set_track_color" type="select" label="Specify track color?">
+            <param name="set_track_color" type="select" label="Select track color?">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
@@ -77,6 +77,20 @@
     </outputs>
     <tests>
         <test>
+            <param name="input">
+                <collection type="list">
+                    <element name="IDEAS_out.cluster" value="IDEAS_out.cluster" ftype="txt"/>
+                    <element name="IDEAS_out.para" value="IDEAS_out.para" ftype="txt"/>
+                    <element name="IDEAS_out.profile" value="IDEAS_out.profile" ftype="txt"/>
+                    <element name="IDEAS_out.state" value="IDEAS_out.state" ftype="txt"/>
+                </collection>
+            </param>
+            <param name="hub_name" value="MyHub"/>
+            <param name="short_label" value="my short label"/>
+            <param name="long_label" value="my long label"/>
+            <param name="set_track_color" value="yes"/>
+            <param name="track_color" value="#ff0000"/>
+            <output name="output_trackhub" file="output_trackhub.html" ftype="trackhub"/>
         </test>
     </tests>
     <help>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/IDEAS_out.cluster	Tue Nov 21 13:23:28 2017 -0500
@@ -0,0 +1,1 @@
+id0 0:0 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/IDEAS_out.para	Tue Nov 21 13:23:28 2017 -0500
@@ -0,0 +1,2 @@
+#count	h3k4me3	h3k4me3*h3k4me3	
+60.000000	0.000000	10.000000	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/IDEAS_out.profile	Tue Nov 21 13:23:28 2017 -0500
@@ -0,0 +1,2 @@
+1 0.958910 
+49 0.980769 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/IDEAS_out.state	Tue Nov 21 13:23:28 2017 -0500
@@ -0,0 +1,51 @@
+#ID CHR POSst POSed e001 PosClass
+R100001 chr1 21819600 21819800 0 0
+R100002 chr1 21819800 21820000 0 1
+R100003 chr1 21820000 21820200 0 1
+R100004 chr1 21820200 21820400 0 1
+R100005 chr1 21820400 21820600 0 1
+R100006 chr1 21820600 21820800 0 1
+R100007 chr1 21820800 21821000 0 1
+R100008 chr1 21821000 21821200 0 1
+R100009 chr1 21821200 21821400 0 1
+R100010 chr1 21821400 21821600 0 1
+R100011 chr1 21821600 21821800 0 1
+R100012 chr1 21821800 21822000 0 1
+R100013 chr1 21822000 21822200 0 1
+R100014 chr1 21822200 21822400 0 1
+R100015 chr1 21822400 21822600 0 1
+R100016 chr1 21822600 21822800 0 1
+R100017 chr1 21822800 21823000 0 1
+R100018 chr1 21823000 21823200 0 1
+R100019 chr1 21823200 21823400 0 1
+R100020 chr1 21823400 21823600 0 1
+R100021 chr1 21823600 21823800 0 1
+R100022 chr1 21823800 21824000 0 1
+R100023 chr1 21824000 21824200 0 1
+R100024 chr1 21824200 21824400 0 1
+R100025 chr1 21824400 21824600 0 1
+R100026 chr1 21824600 21824800 0 1
+R100027 chr1 21824800 21825000 0 1
+R100028 chr1 21825000 21825200 0 1
+R100029 chr1 21825200 21825400 0 1
+R100030 chr1 21825400 21825600 0 1
+R100031 chr1 21825600 21825800 0 1
+R100032 chr1 21825800 21826000 0 1
+R100033 chr1 21826000 21826200 0 1
+R100034 chr1 21826200 21826400 0 1
+R100035 chr1 21826400 21826600 0 1
+R100036 chr1 21826600 21826800 0 1
+R100037 chr1 21826800 21827000 0 1
+R100038 chr1 21827000 21827200 0 1
+R100039 chr1 21827200 21827400 0 1
+R100040 chr1 21827400 21827600 0 1
+R100041 chr1 21827600 21827800 0 1
+R100042 chr1 21827800 21828000 0 1
+R100043 chr1 21828000 21828200 0 1
+R100044 chr1 21828200 21828400 0 1
+R100045 chr1 21828400 21828600 0 1
+R100046 chr1 21829000 21829200 0 1
+R100047 chr1 21829400 21829600 0 1
+R100048 chr1 21829600 21829800 0 1
+R100049 chr1 21829800 21830000 0 1
+R100050 chr1 21830000 21830200 0 1
Binary file test-data/e001-h3k4me3.bigwig has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_trackhub.html	Tue Nov 21 13:23:28 2017 -0500
@@ -0,0 +1,10 @@
+<html>
+    <head>
+    </head>
+    <body>
+        <ul>
+            <li><a href="tracks/MyHub.1.bigbed">tracks/MyHub.1.bigbed</a></li>
+            <li><a href="tracks/trackDb.txt">tracks/trackDb.txt</a></li>
+        </ul>
+    </body>
+</html>
--- a/test-data/test.bed	Tue Nov 21 09:04:59 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-chr1	21819600	21819800	R100001
-chr1	21819800	21820000	R100002
-chr1	21820000	21820200	R100003
-chr1	21820200	21820400	R100004
-chr1	21820400	21820600	R100005
-chr1	21820600	21820800	R100006
-chr1	21820800	21821000	R100007
-chr1	21821000	21821200	R100008
-chr1	21821200	21821400	R100009
-chr1	21821400	21821600	R100010
-chr1	21821600	21821800	R100011
-chr1	21821800	21822000	R100012
-chr1	21822000	21822200	R100013
-chr1	21822200	21822400	R100014
-chr1	21822400	21822600	R100015
-chr1	21822600	21822800	R100016
-chr1	21822800	21823000	R100017
-chr1	21823000	21823200	R100018
-chr1	21823200	21823400	R100019
-chr1	21823400	21823600	R100020
-chr1	21823600	21823800	R100021
-chr1	21823800	21824000	R100022
-chr1	21824000	21824200	R100023
-chr1	21824200	21824400	R100024
-chr1	21824400	21824600	R100025
-chr1	21824600	21824800	R100026
-chr1	21824800	21825000	R100027
-chr1	21825000	21825200	R100028
-chr1	21825200	21825400	R100029
-chr1	21825400	21825600	R100030
-chr1	21825600	21825800	R100031
-chr1	21825800	21826000	R100032
-chr1	21826000	21826200	R100033
-chr1	21826200	21826400	R100034
-chr1	21826400	21826600	R100035
-chr1	21826600	21826800	R100036
-chr1	21826800	21827000	R100037
-chr1	21827000	21827200	R100038
-chr1	21827200	21827400	R100039
-chr1	21827400	21827600	R100040
-chr1	21827600	21827800	R100041
-chr1	21827800	21828000	R100042
-chr1	21828000	21828200	R100043
-chr1	21828200	21828400	R100044
-chr1	21828400	21828600	R100045
-chr1	21829000	21829200	R100046
-chr1	21829400	21829600	R100047
-chr1	21829600	21829800	R100048
-chr1	21829800	21830000	R100049
-chr1	21830000	21830200	R100050