changeset 2:30cdbc4faefa draft default tip

Update galaxy tool to v1.0.1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Wed Jan 24 02:42:53 2018 -0500
@@ -0,0 +1,53 @@
+Galaxy Wrapper for MAnorm
+=========================
+
+Introduction
+------------
+
+ChIP-Seq is widely used to characterize genome-wide binding patterns of
+transcription factors and other chromatin-associated proteins. Although
+comparison of ChIP-Seq data sets is critical for understanding cell
+type-dependent and cell state-specific binding, and thus the study of
+cell-specific gene regulation, few quantitative approaches have been
+developed.
+
+Here, we present a simple and effective method, MAnorm, for quantitative
+comparison of ChIP-Seq data sets describing transcription factor binding
+sites and epigenetic modifications. The quantitative binding differences
+inferred by MAnorm showed strong correlation with both the changes in
+expression of target genes and the binding of cell type-specific
+regulators.
+
+Installation
+------------
+
+Please search and install MAnorm galaxy tool via the `Galaxy Tool Shed`_.
+
+.. _`Galaxy Tool Shed`: https://toolshed.g2.bx.psu.edu/view/haydensun/manorm
+
+Documentation
+-------------
+To see the full documentation of MAnorm, please refer to: http://manorm.readthedocs.io/en/latest/
+
+ChangeLog
+---------
+- v1.0.1: Fix an incorrect file name, related to MAnorm-v1.1.3
+- v1.0: Initial release, related to MAnorm-v1.1.2
+
+
+Links
+-----
+The Python version of MAnorm is developed by ShaoLab_ at `CAS-MPG Partner Institute for Computational Biology, SIBS, CAS`_.
+
+GitHub: https://github.com/shao-lab/MAnorm
+
+.. _ShaoLab: http://bioinfo.sibs.ac.cn/shaolab/
+.. _CAS-MPG Partner Institute for Computational Biology, SIBS, CAS: http://www.picb.ac.cn/picb/indexeng.jsp
+
+
+
+
+
+
+
+

--- a/manorm.xml	Mon Jan 22 04:40:43 2018 -0500
+++ b/manorm.xml	Wed Jan 24 02:42:53 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="manorm" name="MAnorm" version="1.0">
+<tool id="manorm" name="MAnorm" version="1.0.1">
     <description>Quantitative comparison of ChIP-Seq samples</description>
     <requirements>
-        <requirement type="package" version="1.1.2">manorm</requirement>
+        <requirement type="package" version="1.1.3">manorm</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         manorm --p1 $p1 --p2 $p2 --r1 $r1 --r2 $r2 $s --name1 sample1 --name2 sample2 -o output_dir
@@ -76,7 +76,7 @@
             <filter>s == True</filter>
         </data>
         <data name="sample1_biased_peaks" format="bed" label="MAnorm (sample1 biased peaks)" from_work_dir="output_dir/output_filters/sample1_M_above_*_biased_peaks.bed" />
-        <data name="sample2_biased_peaks" format="bed" label="MAnorm (sample2 biased peaks)" from_work_dir="output_dir/output_filters/sample1_M_below_*_biased_peaks.bed" />
+        <data name="sample2_biased_peaks" format="bed" label="MAnorm (sample2 biased peaks)" from_work_dir="output_dir/output_filters/sample2_M_below_*_biased_peaks.bed" />
         <data name="unbiased_peaks" format="bed" label="MAnorm (unbiased peaks)" from_work_dir="output_dir/output_filters/sample1_vs_sample2_unbiased_peaks.bed" />
         <data name="m_value_track" format="wig" label="MAnorm (M values track)" from_work_dir="output_dir/output_tracks/sample1_vs_sample2_M_values.wig" />
         <data name="a_value_track" format="wig" label="MAnorm (A values track)" from_work_dir="output_dir/output_tracks/sample1_vs_sample2_A_values.wig" />