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changeset 4:56e104999978 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
author iuc
date Mon, 06 Feb 2017 02:30:37 -0500
parents 6d4babad010f
children beb902da6e5f
files dir2html.py macs2_bdgdiff.xml macs2_callpeak.xml test-data/output_extra_files.html tool_dependencies.xml
diffstat 5 files changed, 69 insertions(+), 51 deletions(-) [+]
line wrap: on
line diff
--- a/dir2html.py	Wed Jan 27 15:23:25 2016 -0500
+++ b/dir2html.py	Mon Feb 06 02:30:37 2017 -0500
@@ -1,38 +1,43 @@
-#!/usr/bin/env python
-import os
-import sys
-from xml.sax.saxutils import escape
-
-def make_table( directory ):
-    ret = ['<table class="fileList">\n']
-    for file in os.listdir( directory ):
-        ret.append('<tr><td class="file"><a href="%s">%s</a></td></tr>\n' % ( file, escape(file).replace( 'MACS2_', '' ) ))
-    ret.append('</table>')
-    return ''.join(ret)
-
-def make_html( directory, stderr ):
-    return '\n'.join(['<html>'
-                      '<head>',
-                      '   <title>Additional output created by MACS2</title>',
-                      '   <style type="text/css">',
-                      '      table.fileList { text-align: left; }',
-                      '      td.directory { font-weight: bold; }',
-                      '      td.file { padding-left: 4em; }',
-                      '   </style>',
-                      '</head>',
-                      '<body>',
-                      '<h1>Additional Files:</h1>',
-                      make_table( directory ),
-                      '<h3>Messages from MACS2:</h3>',
-                      stderr.read().replace('\n', '<br>'),
-                      '</body>',
-                      '</html>'])
-                   
-if __name__ == '__main__':
-    if len(sys.argv) == 3:
-        directory_path = sys.argv[1]
-        stderr = open( sys.argv[2] )
-        print make_html( directory_path, stderr )
-    else:
-        sys.exit( 'Two parameter expected: directory path and stderr path' )
-
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import os
+import sys
+from xml.sax.saxutils import escape
+
+
+def make_table(directory):
+    ret = ['<table class="fileList">\n']
+    for filename in os.listdir(directory):
+        ret.append('<tr><td class="file"><a href="%s">%s</a></td></tr>\n' % (filename, escape(filename).replace('MACS2_', '')))
+    ret.append('</table>')
+    return ''.join(ret)
+
+
+def make_html(directory, stderr):
+    return '\n'.join(['<html>'
+                      '<head>',
+                      '   <title>Additional output created by MACS2</title>',
+                      '   <style type="text/css">',
+                      '      table.fileList { text-align: left; }',
+                      '      td.directory { font-weight: bold; }',
+                      '      td.file { padding-left: 4em; }',
+                      '   </style>',
+                      '</head>',
+                      '<body>',
+                      '<h1>Additional Files:</h1>',
+                      make_table(directory),
+                      '<h3>Messages from MACS2:</h3>',
+                      stderr.read().replace('\n', '<br>'),
+                      '</body>',
+                      '</html>'])
+
+
+if __name__ == '__main__':
+    if len(sys.argv) == 3:
+        directory_path = sys.argv[1]
+        stderr = open(sys.argv[2])
+        print(make_html(directory_path, stderr))
+    else:
+        sys.exit('Two parameter expected: directory path and stderr path')
--- a/macs2_bdgdiff.xml	Wed Jan 27 15:23:25 2016 -0500
+++ b/macs2_bdgdiff.xml	Mon Feb 06 02:30:37 2017 -0500
@@ -33,11 +33,10 @@
         <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="default: 1 (--depth2)" />
         <param name="maxgap" type="integer" value="100" label="Maximum gap to merge nearby differential regions" help="Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length. Default: 100 (-g)." />
 
-        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs">
+        <param name="outputs" type="select" display="checkboxes" multiple="True" optional="false" label="Outputs">
             <option value="--ofile-cond1">Unique regions in condition 1</option>
             <option value="--ofile-cond2">Unique regions in condition 2</option>
             <option value="--ofile-both-conditions" selected="true">Common regions in both conditions</option>
-            <validator type="no_options" message="Please select at least one output file." />
         </param>
     </inputs>
     <outputs>
--- a/macs2_callpeak.xml	Wed Jan 27 15:23:25 2016 -0500
+++ b/macs2_callpeak.xml	Mon Feb 06 02:30:37 2017 -0500
@@ -66,8 +66,6 @@
             #if str($cutoff_options.pvalue).strip() != '':
                 --pvalue "${ cutoff_options.pvalue }"
             #end if
-        #else:
-            --foldenrichment "${ cutoff_options.foldenrichment }"
         #end if
 
         ## model options
@@ -121,7 +119,6 @@
             <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
                 <option value="qvalue" selected="true">q-value</option>
                 <option value="pvalue">p-value</option>
-                <option value="foldenrichment">foldenrichment</option>
             </param>
             <when value="pvalue">
                 <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection"
@@ -131,10 +128,6 @@
                 <param name="qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection"
                     help="default: 0.05 (--qvalue)"/>
             </when>
-            <when value="foldenrichment">
-                <param name="foldenrichment" value="" type="integer" label="Foldenrichment cutoff for peak detection"
-                    help="(--foldenrichment)"/>
-            </when>
         </conditional>
 
         <conditional name="nomodel_type">
@@ -150,14 +143,13 @@
             </when>
         </conditional>
 
-        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs" help="PDF only created when model is build">
+        <param name="outputs" type="select" display="checkboxes" multiple="True" optional="false" label="Outputs" help="PDF only created when model is build">
             <option value="peaks_tabular" selected="True">Peaks as tabular file</option>
             <!--<option value="narrow">narrow Peaks</option>-->
             <option value="summits" selected="true">summits</option>
             <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option>
             <option value="html">Summary page (html)</option>
             <option value="pdf">Plot in PDF</option>
-            <validator type="no_options" message="Please select at least one output file." />
         </param>
 
         <conditional name="advanced_options">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_extra_files.html	Mon Feb 06 02:30:37 2017 -0500
@@ -0,0 +1,22 @@
+<html><head>
+   <title>Additional output created by MACS2</title>
+   <style type="text/css">
+      table.fileList { text-align: left; }
+      td.directory { font-weight: bold; }
+      td.file { padding-left: 4em; }
+   </style>
+</head>
+<body>
+<h1>Additional Files:</h1>
+<table class="fileList">
+<tr><td class="file"><a href="MACS2_model.pdf">model.pdf</a></td></tr>
+<tr><td class="file"><a href="MACS2_summits.bed">summits.bed</a></td></tr>
+<tr><td class="file"><a href="MACS2_model.r">model.r</a></td></tr>
+<tr><td class="file"><a href="MACS2_peaks.narrowPeak">peaks.narrowPeak</a></td></tr>
+<tr><td class="file"><a href="MACS2_model.r.log">model.r.log</a></td></tr>
+<tr><td class="file"><a href="MACS2_peaks.xls">peaks.xls</a></td></tr>
+</table>
+<h3>Messages from MACS2:</h3>
+INFO  @ Tue, 24 Jan 2017 12:19:10: <br># Command line: callpeak --name MACS2 -t /tmp/tmp1QIUtc/files/000/dataset_1.dat -c /tmp/tmp1QIUtc/files/000/dataset_2.dat --format=BED --gsize 3300000000 --bw=300 --qvalue 0.05<br># ARGUMENTS LIST:<br># name = MACS2<br># format = BED<br># ChIP-seq file = ['/tmp/tmp1QIUtc/files/000/dataset_1.dat']<br># control file = ['/tmp/tmp1QIUtc/files/000/dataset_2.dat']<br># effective genome size = 3.30e+09<br># band width = 300<br># model fold = [5, 50]<br># qvalue cutoff = 5.00e-02<br># Larger dataset will be scaled towards smaller dataset.<br># Range for calculating regional lambda is: 1000 bps and 10000 bps<br># Broad region calling is off<br># Paired-End mode is off<br> <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 read tag files... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 read treatment tags... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1.2 read input tags... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 tag size is determined as 100 bps <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 tag size = 100 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  total tags in treatment: 199977 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 user defined the maximum tags... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  tags after filtering in treatment: 199583 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  Redundant rate of treatment: 0.00 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  total tags in control: 199978 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 user defined the maximum tags... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  tags after filtering in control: 199867 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  Redundant rate of control: 0.00 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 finished! <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #2 Build Peak Model... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #2 looking for paired plus/minus strand peaks... <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #2 number of paired peaks: 4488 <br>INFO  @ Tue, 24 Jan 2017 12:19:11: start model_add_line... <br>INFO  @ Tue, 24 Jan 2017 12:19:11: start X-correlation... <br>INFO  @ Tue, 24 Jan 2017 12:19:11: end of X-cor <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #2 finished! <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #2 predicted fragment length is 254 bps <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #2 alternative fragment length(s) may be 254 bps <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #2.2 Generate R script for model : MACS2_model.r <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #3 Call peaks... <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #3 Pre-compute pvalue-qvalue table... <br>INFO  @ Tue, 24 Jan 2017 12:19:12: #3 Call peaks for each chromosome... <br>INFO  @ Tue, 24 Jan 2017 12:19:13: #4 Write output xls file... MACS2_peaks.xls <br>INFO  @ Tue, 24 Jan 2017 12:19:13: #4 Write peak in narrowPeak format file... MACS2_peaks.narrowPeak <br>INFO  @ Tue, 24 Jan 2017 12:19:13: #4 Write summits bed file... MACS2_summits.bed <br>INFO  @ Tue, 24 Jan 2017 12:19:13: Done! <br>
+</body>
+</html>
--- a/tool_dependencies.xml	Wed Jan 27 15:23:25 2016 -0500
+++ b/tool_dependencies.xml	Mon Feb 06 02:30:37 2017 -0500
@@ -7,13 +7,13 @@
        <repository changeset_revision="cfbbe183f8a7" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="R" version="3.1.2">
-        <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="gnu_awk" version="4.1.0">
        <repository changeset_revision="f145f856ec57" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="macs2" version="2.1.0.20151222">
-       <repository changeset_revision="ae3cfa214a33" name="package_macs2_2_1_0_20151222" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="e1370f7d5e2f" name="package_macs2_2_1_0_20151222" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <set_environment version="1.0">
         <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>