# HG changeset patch
# User saharlcc
# Date 1489747666 14400
# Node ID 630d5a01ef13ce51ddd6aeadf6ccdef42ce1d086
# Parent  78d03bf22a1f534ba4b75ad6799eac57fa309430
Minor change in IsoDE2 interface

diff -r 78d03bf22a1f -r 630d5a01ef13 isoem2_isode2/isoDE.xml
--- a/isoem2_isode2/isoDE.xml	Thu Mar 16 13:44:03 2017 -0400
+++ b/isoem2_isode2/isoDE.xml	Fri Mar 17 06:47:46 2017 -0400
@@ -36,7 +36,7 @@
     </repeat>
 
 
-    <param name="pval" label="p-value" type="float" value="0.05" help="Desired p-value to for which a reliable fold change level will be reported" />
+    <param name="pval" label="Significance level" type="float" value="0.05" help="Desired significance level for which a conservative (reliable) fold change will be reported" />
 
   </inputs>
   <outputs>
@@ -50,13 +50,12 @@
 **What it does**
 
 Computes gene and isoform differential expression between two conditions (example tumor and normal) for both Fragment per Kilobase of transcript length per Million 
-bases (FPKM) and Transcripts per Million (TPM) values. The computation is based on the boostraping output generated by IsoEM2. The number of bootstrap iterations for 
-IsoEM2 should be >= 20 (suggested 200).
+bases (FPKM) and Transcripts per Million (TPM) values. The computation is based on the boostraping output generated by IsoEM2. 
 
 **Input**
 
 * - One or more IsoEM output files (compressed tar files) for each of the two conditions. More than one file can be used if there are replicated for either condition
-* - Desired p-value to for which a reliable fold change level will be reported
+* - Desired Significance level for which a reliable fold change level will be reported
 *
 
 
@@ -66,14 +65,14 @@
 
 * four output files containinag results for Gene FPKM DE, Gene TPM DE, Isoform FPKM DE, and Isoform TPM DE. The four files have identical format with the following fields
 * 1- Gene/isoform ID
-* 2- Reliable log_2(FC) : conservative estimate of fold change in log base 2. 
-*               For the confidence level specified by the input p-value, fold change of gene/isoform abundance (FPKM/TPM) in condition 2 compared condition 1 is 
+* 2- Conservative log_2(FC) : conservative estimate of fold change in log base 2. 
+*               For the confidence level as input, fold change of gene/isoform abundance (FPKM/TPM) in condition 2 compared condition 1 is 
 *               at least 2 ^ absoulte value of this field.The sign indicates the direction, +ve means over expressed in condition 2, -ve means underexpressed in
 *               condition 1. 0 indicates that no change was detected.
-* 3- log_2(condition 2 FPKM (or TPM)/condition 1 FPKM(or TPM)) based on IsoEM2 run without bootstrapping
-* 4- condition 1 FPKM (or TPM) based on IsoEM2 run without bootstrapping
-* 5- condition 2 FPKM (or TPM) based on IsoEM2 run without bootstrapping
-
+* 3- log_2(condition 2 FPKM (or TPM)/condition 1 FPKM(or TPM)) based on IsoEM2 run without bootstrapping (average FPKM or TPM if replicates used)
+* 4- condition 1 FPKM (or TPM) based on IsoEM2 run without bootstrapping (average if replicates used)
+* 5- condition 2 FPKM (or TPM) based on IsoEM2 run without bootstrapping (average if replicates used)
+ 
 
 </help>
 </tool>
diff -r 78d03bf22a1f -r 630d5a01ef13 isoem2_isode2/isoDE2.sh
--- a/isoem2_isode2/isoDE2.sh	Thu Mar 16 13:44:03 2017 -0400
+++ b/isoem2_isode2/isoDE2.sh	Fri Mar 17 06:47:46 2017 -0400
@@ -141,7 +141,7 @@
 date
 
 
-awk '{if (NR == 1) {print "Gene ID\tConfident log2 FC\t Single run log2 FC\t c1 FPKM\tc2 FPKM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t"  $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${geneFPKMout_file}
+awk '{if (NR == 1) {print "Gene ID\tConservative log2 FC\t Single run log2 FC\t c1 average FPKM\tc2 average FPKM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t"  $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${geneFPKMout_file}
 
 cd ..
 
@@ -164,7 +164,7 @@
 echo awk command
 date
 pwd
-awk '{if (NR == 1) {print "Isoform ID\tConfident log2 FC\t Single run log2 FC\t c1 FPKM\tc2 FPKM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t"  $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt  > ${isoFPKMout_file}
+awk '{if (NR == 1) {print "Isoform ID\tConservative log2 FC\t Single run log2 FC\t c1 average FPKM\tc2 average FPKM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t"  $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt  > ${isoFPKMout_file}
 cd ..
 
 
@@ -184,7 +184,7 @@
 echo awk command
 date
 pwd
-awk '{if (NR == 1) {print "Gene ID\tConfident log2 FC\t Single run log2 FC\t c1 TPM\tc2 TPM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t"  $5 "\t" $6 "\t" $7}}'  Bootstrap_Merge1_DIR/output.txt  > ${geneTPMout_file}
+awk '{if (NR == 1) {print "Gene ID\tConservative log2 FC\t Single run log2 FC\t c1 average TPM\tc2 average TPM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t"  $5 "\t" $6 "\t" $7}}'  Bootstrap_Merge1_DIR/output.txt  > ${geneTPMout_file}
 cd ..
 
 
@@ -204,7 +204,7 @@
 echo awk command
 date
 
-awk '{if (NR == 1) {print "Isoform ID\tConfident log2 FC\t Single run log2 FC\t c1 TPM\tc2 TPM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t"  $5 "\t" $6 "\t" $7}}'  Bootstrap_Merge1_DIR/output.txt  > ${isoTPMout_file}
+awk '{if (NR == 1) {print "Conservative Isoform ID\tConfident log2 FC\t Single run log2 FC\t c1 average TPM\tc2 average TPM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t"  $5 "\t" $6 "\t" $7}}'  Bootstrap_Merge1_DIR/output.txt  > ${isoTPMout_file}
 
 cd ..