# HG changeset patch
# User lldelisle
# Date 1666169418 0
# Node ID 05aa21d39189fb3bd442cd570de06c6feacbbf5f

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty

diff -r 000000000000 -r 05aa21d39189 revertR2orientationInBam.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/revertR2orientationInBam.sh	Wed Oct 19 08:50:18 2022 +0000
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+inputBam=$1
+outputBam=$2
+
+samtools view -h "$inputBam" | awk -v OFS="\t" '{
+    # Process only non header lines
+    if(!($1~/^@/)){
+        # SAM flag is field 2
+        n=$2
+        # Change only the second in pair flag is 128
+        d=128
+        q=(n-n%d)/d+(n<0)
+        if(q%2==1){
+            # Evaluate the strand reverse strand flag is 16
+            d=16
+            q=(n-n%d)/d+(n<0)
+            if(q%2==1){
+                # It is reverse it is now forward
+                $2-=16
+            }else{
+                # It is forward it is now reverse
+                $2+=16
+            }
+        }
+    }
+    print
+}' | samtools view -b - > "$outputBam"
\ No newline at end of file
diff -r 000000000000 -r 05aa21d39189 revertR2orientationInBam.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/revertR2orientationInBam.xml	Wed Oct 19 08:50:18 2022 +0000
@@ -0,0 +1,40 @@
+<tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.1" profile="16.04">
+  <description> Revert the mapped orientation of R2 mates in a bam.</description>
+  <requirements>
+    <requirement type="package" version="1.9">samtools</requirement>
+  </requirements>
+  <stdio>
+    <!-- Anything other than zero is an error -->
+    <exit_code range="1:" />
+    <exit_code range=":-1" />
+    <!-- In case the return code has not been set propery check stderr too -->
+    <regex match="Error:" />
+    <regex match="Exception:" />
+  </stdio>
+  <command>
+<![CDATA[
+        bash $__tool_directory__/revertR2orientationInBam.sh $input $output
+]]>
+  </command>
+  <inputs>
+    <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
+    <param name="input" type="data" format="sam,bam" label="Select a sam or bam file."/>
+  </inputs>
+  <outputs>
+    <data format="bam" name="output" label="$input.name with R2 orientation reversed"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="input.sam"/>
+      <output name="output" file="output.bam" ftype="bam"/>
+    </test>
+  </tests>  
+  <help>
+<![CDATA[
+    This tool is very useful when you have paired-end stranded RNA-seq.
+    Using this tool prior to a bedtools genome coverage allow to have strand specific coverage using both mates.
+    It uses samtools to convert input to sam format and then awk to modify the flag "reverse strand" for the second mate of pairs.
+]]>
+  </help>
+</tool>
diff -r 000000000000 -r 05aa21d39189 test-data/input.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.sam	Wed Oct 19 08:50:18 2022 +0000
@@ -0,0 +1,7 @@
+@HD	VN:1.4	SO:coordinate
+@SQ	SN:chr1	LN:195471971
+1	163	chr1	3151308	255	43M	=	3151560	295	GTCCCAAAAAGCAGAGAGAAATATCTCTCTGGGCCTTATAGCA	AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	NH:i:1 HI:i:1 AS:i:82 nM:i:1
+1	83	chr1	3151560	255	43M	=	3151308	-295	CTGCTGGAAAAACTGTTCGTTTTAGGAAATAAGGGCGAGTGCG	EEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAAAAA	NH:i:1 HI:i:1 AS:i:82 nM:i:1
+2	137	chr1	3155261	255	9S20M	*	0	0	TGTGGGTTTTACACACGGGAGGAATCGGG	AAAAA/EEE/EE6EAEE6EAE6/EEEAEE	NH:i:1 HI:i:1 AS:i:19 nM:i:0
+3	99	chr1	3195817	255	43M	=	3195911	137	ATCTTACTCTGTTTCACAGATAGGTGCTGAGGTTAAATTTTGC	AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	NH:i:1 HI:i:1 AS:i:84 nM:i:0
+3	147	chr1	3195911	255	43M	=	3195817	-137	GGTGTAGGTTCTTAGACGCAAGAAATCTCAGGTAGAGTTTGGC	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA	NH:i:1 HI:i:1 AS:i:84 nM:i:0
diff -r 000000000000 -r 05aa21d39189 test-data/output.bam
Binary file test-data/output.bam has changed