| Previous changeset 1:52225f471c57 (2018-01-22) |
|
Commit message:
Update galaxy tool to v1.0.1 |
|
modified:
manorm.xml |
|
added:
README.rst |
| b |
| diff -r 52225f471c57 -r 30cdbc4faefa README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Jan 24 02:42:53 2018 -0500 |
| b |
| @@ -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 + + + + + + + + |
| b |
| diff -r 52225f471c57 -r 30cdbc4faefa manorm.xml --- 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" /> |