# HG changeset patch
# User jjohnson
# Date 1658852493 0
# Node ID 74af9ab1a1549046df9fb53cd1a355ddf0fd94ba
# Parent  ff15d6def09b6f1955fb2bb61aa2f76f96395cb9
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 77429eedace24dcb2ebf8e209fce1515d2adb055-dirty"

diff -r ff15d6def09b -r 74af9ab1a154 rmats.xml
--- a/rmats.xml	Sat Jul 23 21:23:48 2022 +0000
+++ b/rmats.xml	Tue Jul 26 16:21:33 2022 +0000
@@ -256,14 +256,72 @@
 
     </tests>
     <help><![CDATA[
-** rMATS **
+**rMATS**
 
 RMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.
 
+
+**INPUTS**
+
+BAM files
+
+Reads can be mapped independently of rMATS with any aligner and then the resulting BAM files can be used as input to rMATS. rMATS requires aligned reads to match --readLength unless --variable-read-length is given. rMATS also ignores alignments with soft or hard clipping unless --allow-clipping is given.
+
 https://github.com/Xinglab/rmats-turbo#starting-with-bam-files
 
+
+**OUTPUTS**
+
 https://github.com/Xinglab/rmats-turbo#output
 
+**Splicing Events**
+
+.. image:: rmats_diagram.png
+  :height: 562
+  :width: 815
+
+
+Each alternative splicing event type has a corresponding set of output files. In the filename templates below [AS_Event] is replaced by one of [SE (skipped exon), MXE (mutually exclusive exons), A3SS (alternative 3' splice site), A5SS (alternative 5' splice site), RI (retained intron)] for the event specific filename.
+
+
+Output Files:
+  * summary.txt: Brief summary of all AS event types. Includes the total event counts and significant event counts. By default, events are counted as significant if FDR <= 0.05. 
+  * [AS_Event].MATS.JC.txt: Final output including only reads that span junctions defined by rmats (Junction Counts)
+  * [AS_Event].MATS.JCEC.txt: Final output including both reads that span junctions defined by rmats (Junction Counts) and reads that do not cross an exon boundary (Exon Counts)
+  * fromGTF.[AS_Event].txt: All identified alternative splicing (AS) events derived from GTF and RNA
+  * fromGTF.novelJunction.[AS_Event].txt: Alternative splicing (AS) events which were identified only after considering the RNA (as opposed to analyzing the GTF in isolation). This does not include events with an unannotated splice site.
+  * fromGTF.novelSpliceSite.[AS_Event].txt: This file contains only those events which include an unannotated splice site. Only relevant if --novelSS is enabled.
+  * JC.raw.input.[AS_Event].txt: Event counts including only reads that span junctions defined by rmats (Junction Counts)
+  * JCEC.raw.input.[AS_Event].txt: Event counts including both reads that span junctions defined by rmats (Junction Counts) and reads that do not cross an exon boundary (Exon Counts)
+
+Shared columns:
+  * ID: rMATS event id
+  * GeneID: Gene id
+  * geneSymbol: Gene name
+  * chr: Chromosome
+  * strand: Strand of the gene
+  * IJC_SAMPLE_1: Inclusion counts for sample 1. Replicates are comma separated
+  * SJC_SAMPLE_1: Skipping counts for sample 1. Replicates are comma separated
+  * IJC_SAMPLE_2: Inclusion counts for sample 2. Replicates are comma separated
+  * SJC_SAMPLE_2: Skipping counts for sample 2. Replicates are comma separated
+  * IncFormLen: Length of inclusion form, used for normalization
+  * SkipFormLen: Length of skipping form, used for normalization
+  * PValue: Significance of splicing difference between the two sample groups. (Only available if the statistical model is on)
+  * FDR: False Discovery Rate calculated from p-value. (Only available if statistical model is on)
+  * IncLevel1: Inclusion level for sample 1. Replicates are comma separated. Calculated from normalized counts
+  * IncLevel2: Inclusion level for sample 2. Replicates are comma separated. Calculated from normalized counts
+  * IncLevelDifference: average(IncLevel1) - average(IncLevel2)
+Event specific columns (event coordinates):
+  * SE: exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE
+    + The inclusion form includes the target exon (exonStart_0base, exonEnd)
+  * MXE: 1stExonStart_0base 1stExonEnd 2ndExonStart_0base 2ndExonEnd upstreamES upstreamEE downstreamES downstreamEE
+    + If the strand is + then the inclusion form includes the 1st exon (1stExonStart_0base, 1stExonEnd) and skips the 2nd exon
+    + If the strand is - then the inclusion form includes the 2nd exon (2ndExonStart_0base, 2ndExonEnd) and skips the 1st exon
+  * A3SS, A5SS: longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
+    + The inclusion form includes the long exon (longExonStart_0base, longExonEnd) instead of the short exon (shortES shortEE)
+  * RI: riExonStart_0base riExonEnd upstreamES upstreamEE downstreamES downstreamEE
+    + The inclusion form includes (retains) the intron (upstreamEE, downstreamES)
+
     ]]></help>
     <expand macro="citations" />
 </tool>
diff -r ff15d6def09b -r 74af9ab1a154 static/images/rmats_diagram.png
Binary file static/images/rmats_diagram.png has changed