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changeset 1:51b4590a972d draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 98f4b00d71cbc2dd15fc633a6cc3246235308e46
author artbio
date Mon, 18 Sep 2017 17:22:07 -0400
parents f6f0f1e5e940
children 15e3e29f310e
files edger-repenrich.xml repenrich.xml
diffstat 2 files changed, 53 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/edger-repenrich.xml	Wed Aug 02 05:17:29 2017 -0400
+++ b/edger-repenrich.xml	Mon Sep 18 17:22:07 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="edger-repenrich" name="edgeR-repenrich" version="1.4.0">
+<tool id="edger-repenrich" name="edgeR-repenrich" version="1.4.1">
     <description>Determines differentially expressed features from RepEnrich counts</description>
     <requirements>
         <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
@@ -130,11 +130,46 @@
 
 **What it does**
 
-Estimate Distance between samples (MDS) and Biological Coefficient Variation (BCV) in count data from high-throughput sequencing assays and test for differential expression using edgeR_.
+Estimate Distance between samples (MDS) and Biological Coefficient Variation (BCV) in count
+data from high-throughput sequencing assays and test for differential expression using edgeR_.
 
 **Inputs**
 
-edger-repenrich takes count tables generated by repenrich as input. Count tables must be generated for each sample individually. Here, edgeR_ is handling a single factor (genotype, age, treatment, etc) that effect your experiment. This factor has two levels/states (for instance, "wild-type" and "mutant".
+edger-repenrich takes count tables generated by repenrich as inputs. A repenrich count table looks
+like:
+
+============== ========== ========== ==========
+LSU-rRNA_Dme    rRNA       rRNA       3659329
+-------------- ---------- ---------- ----------
+FW3_DM          LINE       Jockey     831
+-------------- ---------- ---------- ----------
+DMTOM1_LTR      LTR        Gypsy      1004
+-------------- ---------- ---------- ----------
+R1_DM           LINE       R1         7343
+-------------- ---------- ---------- ----------
+TAHRE           LINE       Jockey     4560
+-------------- ---------- ---------- ----------
+G4_DM           LINE       Jockey     3668
+-------------- ---------- ---------- ----------
+BS              LINE       Jockey     7296
+-------------- ---------- ---------- ----------
+Stalker2_I-int  LTR        Gypsy      12252
+-------------- ---------- ---------- ----------
+Stalker3_LTR    LTR        Gypsy      593
+-------------- ---------- ---------- ----------
+TABOR_I-int     LTR        Gypsy      3947
+-------------- ---------- ---------- ----------
+G7_DM           LINE       Jockey     162
+-------------- ---------- ---------- ----------
+BEL_I-int       LTR        Pao        23757
+-------------- ---------- ---------- ----------
+Gypsy6_I-int    LTR        Gypsy      7489
+============== ========== ========== ==========
+
+Count tables must be
+generated for each sample individually. Here, edgeR_ is handling a single factor
+(genotype, age, treatment, etc) that effect your experiment. This factor has two
+levels/states (for instance, "wild-type" and "mutant".
 You need to select appropriate count table from your history for each factor level.
 
 The following table gives some examples of factors and their levels:
@@ -151,7 +186,15 @@
 Gender    Female         Male
 ========= ============== ===============
 
-*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples.
+*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2.
+Here the order of factor levels is important. For example, for the factor 'Treatment' given
+in above table, edgeR computes fold changes of 'Treated' samples against 'Untreated',
+i.e. the values correspond to up or down regulations of genes in Treated samples.
+
+*Number of aligned reads*:
+
+A file containing the number of reads aligned to transposons by repenrich must me provided
+to edger-repenrich. This file is a single-column tabular file containing a single value.
 
 **Output**
 
--- a/repenrich.xml	Wed Aug 02 05:17:29 2017 -0400
+++ b/repenrich.xml	Mon Sep 18 17:22:07 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="repenrich" name="RepEnrich" version="1.4.0">
+<tool id="repenrich" name="RepEnrich" version="1.4.1">
     <description>Repeat Element Profiling</description>
     <requirements>
         <requirement type="package" version="1.2.0">bowtie</requirement>
@@ -163,7 +163,11 @@
  
 **Outputs**
 
-(1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned in tabular format, for further statistical tests differential expression analysis or graphics 
+(1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned in tabular format,
+for further statistical tests differential expression analysis or graphics.
+
+The "aligned_reads.tab" output file contains a single value corresponding to the number of reads that were aligned to
+transposons. This value is used in downstream analysis by the edger-repenrich tool.
 
 **RepEnrich**