Mercurial > repos > iuc > macs2

changeset 15:d89001e78ee4 draft

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Uploaded
author bgruening
date Fri, 24 Jan 2014 11:18:29 -0500
parents 50f87b0c55bd
children d9a0a017896a
files macs2_filterdup.xml macs2_macros.xml macs2_predictd.xml macs2_randsample.xml tool_dependencies.xml
diffstat 5 files changed, 10 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/macs2_filterdup.xml	Fri Jan 24 11:06:57 2014 -0500
+++ b/macs2_filterdup.xml	Fri Jan 24 11:18:29 2014 -0500
@@ -12,7 +12,7 @@
 
         --format '$ifile.extension.upper()'
         --gsize $gsize
-        --tsize $tsize
+        @tag_size@
         --pvalue $pvalue
         #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
             --keep-dup $keep_dup_options.user_keepdup
--- a/macs2_macros.xml	Fri Jan 24 11:06:57 2014 -0500
+++ b/macs2_macros.xml	Fri Jan 24 11:18:29 2014 -0500
@@ -37,6 +37,11 @@
     <xml name="tag_size">
         <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will overide the auto detected tag size. DEFAULT: Not set (-1.0)  (--tsize)" />
     </xml>
+    <token name="@tag_size@">
+        #if $tsize == -1.0:
+            --tsize $tsize
+        #end if
+    </token>
 
     <xml name="stdio">
         <stdio>
--- a/macs2_predictd.xml	Fri Jan 24 11:06:57 2014 -0500
+++ b/macs2_predictd.xml	Fri Jan 24 11:18:29 2014 -0500
@@ -10,7 +10,7 @@
     <command>
         macs2 predictd
             -i #echo ','.join( map( str, $infiles) )#
-            --tsize $tsize
+            @tag_size@
             @effective_genome_size@
             --bw $band_width
             --mfold $mfoldlo $mfoldhi
--- a/macs2_randsample.xml	Fri Jan 24 11:06:57 2014 -0500
+++ b/macs2_randsample.xml	Fri Jan 24 11:18:29 2014 -0500
@@ -12,7 +12,7 @@
 
         --format '$ifile.extension.upper()'
 
-        --tsize $tsize
+        @tag_size@
         #if str($method_options.method_options_selector ) == 'percentage':
             $method_options.percentage
         #else:
--- a/tool_dependencies.xml	Fri Jan 24 11:06:57 2014 -0500
+++ b/tool_dependencies.xml	Fri Jan 24 11:18:29 2014 -0500
@@ -17,6 +17,8 @@
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/taoliu/MACS.git</action>
+                <!-- Galaxy tries to change automatically to the directory "macs2" (name of the package). 
+                But we need to change to MACS. Go one level back and enter MACS -->
                 <action type="change_directory">../MACS</action>
                 <action type="shell_command">git checkout 7ccb571d2f2dcb5be1d75f323b1d17a59b926deb</action>
                 <action type="shell_command">git submodule update --recursive</action>