# HG changeset patch
# User jpayne
# Date 1512573975 18000
# Node ID 6325216db1fe5d8a8b4eb95be063433eac3c7bc6

planemo upload

diff -r 000000000000 -r 6325216db1fe paired_bam_dealer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/paired_bam_dealer.xml	Wed Dec 06 10:26:15 2017 -0500
@@ -0,0 +1,45 @@
+<tool id="paired_bam_dealer" name="Deal out" version="0.1.0">
+	<description>paired-end reads by alignment or non-alignment to a reference</description>
+    <requirements>
+    	<requirement type="package" version="1.2">samtools</requirement>
+    	<requirement type="package" version="2.26">bedtools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        bamToFastq -i <(samtools sort -n <(samtools view -u -f 1 -F 12 $input_bam  )) 
+        	-fq $mapped_1
+        	-fq2 $mapped_2		&& 	echo "mapped out"	&&
+        bamToFastq -i <(
+        	samtools merge -u -
+        					  <(samtools view -u -f 4  -F 264 $input_bam)
+        					  <(samtools view -u -f 8  -F 260 $input_bam)
+        					  <(samtools view -u -f 12 -F 256 $input_bam)
+        		| samtools sort -n 
+        	)
+        	-fq $unmapped_1
+        	-fq2 $unmapped_2	&& echo "unmapped out"
+    ]]></command>
+    <inputs>
+    	<param format="bam" name="input_bam" type="data" label="BAM alignment" />
+    </inputs>
+    <outputs>
+    	<data format="fastqsanger" label="unmapping reads, reverse" name="unmapped_2" />
+    	<data format="fastqsanger" label="unmapping reads, forward" name="unmapped_1" />
+    	<data format="fastqsanger" label="mapping reads, reverse" name="mapped_2" />
+    	<data format="fastqsanger" label="mapping reads, forward" name="mapped_1" />
+    </outputs>
+    <tests>
+    	<test>
+    		<param name="input_bam" value="mapped_reads.bam" />
+    		<output name="mapped_1" value="forward_mapped.fastq" />
+    		<output name="mapped_2" value="reverse_mapped.fastq" />
+    		<output name="unmapped_1" value="forward_unmapped.fastq" />
+    		<output name="unmapped_2" value="reverse_unmapped.fastq" />
+    	</test>
+    </tests>
+    <help><![CDATA[
+        Input is a BAM alignment of paired-end reads to a reference. Output is paired-end files of reads mapping and reads not mapping to reference.
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 6325216db1fe test-data/forward.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/forward.fastq	Wed Dec 06 10:26:15 2017 -0500
@@ -0,0 +1,16 @@
+@SRR6244075.1/1
+ACCCGCAGCTGTTTACCTCCGGCACCACCTATGACGCCTCTTCCGTACCGCTTTATAACCGCCTGGTTGAATTTAAAATCGGCACCACTGAAGTGATCCCGGGCCTCGCTGAAAAGTGGGAAGTCAGCGAAGACGGTAAAACCTATACCTTCCATCTGCGTAAAGGTGTGAAGTGGCACGACAATAAAGAATTCAAACCGACGCGTGAACTGAACGCCGATGACGTGGTGTTCTCG
++
+1>>>1>11>C1FGG3FBGEA00A0AA0AAG1G12A/AEGEGHFE/F0AF/AEEGBG22FE/EEE//FF/02BGG2211FF////>E0FGBB11FB2GFDE///<<FA//F//1110@F1//FAF1<11<//@.<A.AEAF1D<C/D0D0DDCC0=<G0C:A...:0:/CCB;0CF0./0;.---;09F9;.CFFF00C99--->-@---9;B///99=@-@A//-A--E-AA/9/-
+@SRR6244075.2/1
+GCACAGTTCCCGCAAAAATTTTTCGCCTGACTGCCCGTCGTCATAGCTGGCGTGCAGGGCGCTCATAACATCAGCCACGGTAACCACAATCACTGTCTGACCGTCTTTCAGCAGGCGATTCCCGATAGCTGCCGCTAAGTGATTCTTCCCGGTACCAGGTTTTCCGCTGAACGCAAAATTTGTACACCCGGTCATCAGTTCATCGGCGATGGATTTCGCCTGGCTTAACGCGTATCGCTGGCCGTCGTT
++
+111>11BFD@B1AAA100BFGGHE0AAE00BB1AAA/EE/AA/F22AD10//B/A/10/?/>EE/FB2FDFE11FEA>//?/ABE1F/AFG1FGFHFHB1FF@EEHGHGB2B10////>GD2FA/>/ADGDFG?CC?.1FFBFGFHHF<CA-A-AC00.CGGGCF.AE-.09..--9/;FG0CF909/:--;@?FBBBFFFBFF/-9--9--/BFFB--9A--9BFF/9--@@;BA-9F---9-;=-@B
+@SRR6244075.13/1
+CTTCTGCACCAGTTTGGTCTGGAAAGGCTGCAGGTTCGGCATCTTGTCGGTCAGCAAGCCAAAGCGATCGACCATAAAGACTTTCTGCCGCGCCGCTTCCTCGCTTAATCCTTCGCGCTGGGTCTGGGAGATGATCATTTCGGCAATGCCGCATCCCGCTGTACCTGCGCCAAGGAAGACGATTTTTTTCTCGCTTAACTGACCACCTGCCGCGCGGCTTGCTGCGATCAGTGTGCCGACTGTTACCGCC
++
+AAAAA1D3BCB1BFGFAGEG1111100010A010BFF?0A/AFGH2FE//AA/01100/B00A0A//??//>>/B11111>FEHFHBBD/>/E>E@EECFDEACFH/1BBGHFH/A//<///FCC0000..><1FD1FHHFB----<0<<-:-C@CE?CC?.00;F09-?A.-.../..9;-;EEFF@@FFF--EF-//B//9;BA-A/;A--9;=->@@=-B//--;;-/;/;/999-9@-;BB/;:9@
+@SRR6244075.21/1
+CTACATCCGTCAGCGCGAGTTTTCTACGCTGCGTCTTTCTATGCAGTTGTCGATTGTGGCGGGTTGGCTCCAACCCCCCGCCGATGCCCCCCCAGGGGGGGGGGGTGGATTTTTCTTTCCCCCTCATTTCTTTTTCCCCCTTCAATATTTTTTTGGCGAAATTTTTTTTTGTATTTACCTTACCCCCCCCCTTTTTGGCGGACAGCAGAAGCAGGGGGAGGGAGATATTTCCCCCTTTCTTTACCAACA
++
+CBBCCFFFCCFCGGGGGCEGGGHHHHHGGGGGGGGGGHGHFGFGGBHHHHHGHGHGHHGGCC/>1//333/333/?////<///<//?0/<--<<..<@--:------./;B////:///;;.-.;//:///9:///::A-./:;///:///-;--/--:;.;FF9-:---;//9//////::/:.--;---./:/--/--9-;.A/.///://.-------...////:/;//.-.//://99///.;
diff -r 000000000000 -r 6325216db1fe test-data/forward_mapped.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/forward_mapped.fastq	Wed Dec 06 10:26:15 2017 -0500
@@ -0,0 +1,8 @@
+@SRR6244075.1/1
+ACCCGCAGCTGTTTACCTCCGGCACCACCTATGACGCCTCTTCCGTACCGCTTTATAACCGCCTGGTTGAATTTAAAATCGGCACCACTGAAGTGATCCCGGGCCTCGCTGAAAAGTGGGAAGTCAGCGAAGACGGTAAAACCTATACCTTCCATCTGCGTAAAGGTGTGAAGTGGCACGACAATAAAGAATTCAAACCGACGCGTGAACTGAACGCCGATGACGTGGTGTTCTCG
++
+1>>>1>11>C1FGG3FBGEA00A0AA0AAG1G12A/AEGEGHFE/F0AF/AEEGBG22FE/EEE//FF/02BGG2211FF////>E0FGBB11FB2GFDE///<<FA//F//1110@F1//FAF1<11<//@.<A.AEAF1D<C/D0D0DDCC0=<G0C:A...:0:/CCB;0CF0./0;.---;09F9;.CFFF00C99--->-@---9;B///99=@-@A//-A--E-AA/9/-
+@SRR6244075.2/1
+GCACAGTTCCCGCAAAAATTTTTCGCCTGACTGCCCGTCGTCATAGCTGGCGTGCAGGGCGCTCATAACATCAGCCACGGTAACCACAATCACTGTCTGACCGTCTTTCAGCAGGCGATTCCCGATAGCTGCCGCTAAGTGATTCTTCCCGGTACCAGGTTTTCCGCTGAACGCAAAATTTGTACACCCGGTCATCAGTTCATCGGCGATGGATTTCGCCTGGCTTAACGCGTATCGCTGGCCGTCGTT
++
+111>11BFD@B1AAA100BFGGHE0AAE00BB1AAA/EE/AA/F22AD10//B/A/10/?/>EE/FB2FDFE11FEA>//?/ABE1F/AFG1FGFHFHB1FF@EEHGHGB2B10////>GD2FA/>/ADGDFG?CC?.1FFBFGFHHF<CA-A-AC00.CGGGCF.AE-.09..--9/;FG0CF909/:--;@?FBBBFFFBFF/-9--9--/BFFB--9A--9BFF/9--@@;BA-9F---9-;=-@B
diff -r 000000000000 -r 6325216db1fe test-data/forward_unmapped.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/forward_unmapped.fastq	Wed Dec 06 10:26:15 2017 -0500
@@ -0,0 +1,8 @@
+@SRR6244075.13/1
+CTTCTGCACCAGTTTGGTCTGGAAAGGCTGCAGGTTCGGCATCTTGTCGGTCAGCAAGCCAAAGCGATCGACCATAAAGACTTTCTGCCGCGCCGCTTCCTCGCTTAATCCTTCGCGCTGGGTCTGGGAGATGATCATTTCGGCAATGCCGCATCCCGCTGTACCTGCGCCAAGGAAGACGATTTTTTTCTCGCTTAACTGACCACCTGCCGCGCGGCTTGCTGCGATCAGTGTGCCGACTGTTACCGCC
++
+AAAAA1D3BCB1BFGFAGEG1111100010A010BFF?0A/AFGH2FE//AA/01100/B00A0A//??//>>/B11111>FEHFHBBD/>/E>E@EECFDEACFH/1BBGHFH/A//<///FCC0000..><1FD1FHHFB----<0<<-:-C@CE?CC?.00;F09-?A.-.../..9;-;EEFF@@FFF--EF-//B//9;BA-A/;A--9;=->@@=-B//--;;-/;/;/999-9@-;BB/;:9@
+@SRR6244075.21/1
+CTACATCCGTCAGCGCGAGTTTTCTACGCTGCGTCTTTCTATGCAGTTGTCGATTGTGGCGGGTTGGCTCCAACCCCCCGCCGATGCCCCCCCAGGGGGGGGGGGTGGATTTTTCTTTCCCCCTCATTTCTTTTTCCCCCTTCAATATTTTTTTGGCGAAATTTTTTTTTGTATTTACCTTACCCCCCCCCTTTTTGGCGGACAGCAGAAGCAGGGGGAGGGAGATATTTCCCCCTTTCTTTACCAACA
++
+CBBCCFFFCCFCGGGGGCEGGGHHHHHGGGGGGGGGGHGHFGFGGBHHHHHGHGHGHHGGCC/>1//333/333/?////<///<//?0/<--<<..<@--:------./;B////:///;;.-.;//:///9:///::A-./:;///:///-;--/--:;.;FF9-:---;//9//////::/:.--;---./:/--/--9-;.A/.///://.-------...////:/;//.-.//://99///.;
diff -r 000000000000 -r 6325216db1fe test-data/mapped_reads.bam
Binary file test-data/mapped_reads.bam has changed
diff -r 000000000000 -r 6325216db1fe test-data/reverse.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reverse.fastq	Wed Dec 06 10:26:15 2017 -0500
@@ -0,0 +1,16 @@
+@SRR6244075.1/2
+CTAGAACACCACGTCATCGTCGTTCAGTTCACGCGTCGGTTTGAATTCTTTATTGTCGTGCCACTTCACACCTTTACGCAGATGGAAGGTATAGGTTTTACCGTCTTCGCTGACTTCCCACTTTTCAGCGAGGCCCGGTTTCACTTCATTGGTGCCGTTTTTAAATTCAACCAGGCGGTTTTTAAGCGGTACGGAAGAGTCTTCATAGTTGTTTCCGGAGGTAATCAGCTTCGGTTCTTTCTCTTTTTCA
++
+111111@1>>1>1AA1BF10A0AEE13DGE2A000AA//ABE/11DFFFGG2DE1GE/B//>1BFFE2B21?GGHBF/>///B11010/B1B221BFGFED1/F<FFE//E//BGG><C1BGHHHD22>////<////-.<111>F111<11=.</-.<<EGA00;;:00:.;..:--9;.C..000--;.9.---99-////9/9///;//--;/-----;///////9//-----9/:///;B/9///
+@SRR6244075.2/2
+TTTTATTCTCGTTTGCGAATTACCAGGTGCAGAACGTCGGCCAGCGATACGCGTTAATCCATTCGAAATCCATCGCCGATGAACTGATGACCGGGTGTACAAATTTTGCGTTCAGCGGAAAACCTGGTACCGGGTAGATTCACTTAGCTGCAGCTATCGGGTATCGCCTGCTGAAAGACGGTCAGACAGTGTTTGTGGTTACCGTGGCTGTTGTTATTAGCGCCCTGCACGCCATCTATTACGTCGGGCTT
++
+1>111B33@31>FF11110AA11A110B111110A00A//A///A//B/A/A/>>//2@B1222220/BB11BB//>//>/11>F11B12BB///?/>12211BFGG21/CC<12>/////00?>00>11<.--.<.00==0=DH00<00////;0;/.--.-:9.9.9.9C00000/9..C../09//;//;;/;--:A//B-;---9--;/BE/9////---99---/-----/9/;///---------
+@SRR6244075.13/2
+TTATTAATTTGATTGTGTTTACTGACGGTGAACGTATTCTAGGTCTTGGTGACCATGTCATCTTCGGTTTTTTCCTTTTTTTTTTTTTACTTTTTCTTTTTTCCCCCTTTTTTGGCTTCCTCCCCTTGTTTTTCCTTTTTTTTTTTCTTTATTTTTGTACTCATCACCCTCAGCTTCTTTTCTTTCCTCTTTTTTTTGTTCTGCGTAATTCTCTGTTCTCTTTCTCCTTTTTCTTTTTTTTTTTTGTTTTT
++
+1>1>>3333@33BB1B31B131B33B00A00110A0DF2D22111DF11A/11A111222DD222//A/A///011D211/>///>>//11>>110>1>>1/0110//0111///11001110//00011>0.0<1<111------/090090000-9;00090000/....9/0000090000///////9/;-@-9--/9//-9---//;B/:;9//////9//////:/99/9;9=-;9--;-:-9--
+@SRR6244075.21/2
+TCGTCGCATCCTGAATGCGCAACAGATTAGCCTGCAATTTGTCGCCTGCCGCTTCCAGCGTATCCTGCAATTCACGCAGCGTCCCGGAAGTTTCCGAAAGCAACAATTCACAGCTGGAAATCGCCGCCCGCCAGTCTTTGTTCAGCAACTGGGCGATATCGTCCTTCACCTGCTGCTGCTGTTCGTCCATCAGACGTTGCGTCAGGTCGATACTGTCGAAAATTTCTGCTACCGAATATTTCAGTGGCG
++
+>>3AA@D2A@FFCB4FGFAECEECF3GHC3FGGAGGFGHH5GGEHDGHHF?EEGEGEEGCFFGFHHHHFFGHGBEAG?EEEGGEFGGGCDGHHHHFGDCGGGFFFHHHHFHFHHHHGEFFGHGEGCCDCDGGGGHHHHHFHHHBFHHBGHHBAGGCGDGHGHFGGGGGGFFGGGGGGGFGGGGGDGGGBFGFF0F=EFFD?FBFF.FFB-A.@FFFFFEA.9FFFFFFFFFFF?B9A.FFFFFBBFBA9
diff -r 000000000000 -r 6325216db1fe test-data/reverse_mapped.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reverse_mapped.fastq	Wed Dec 06 10:26:15 2017 -0500
@@ -0,0 +1,8 @@
+@SRR6244075.1/2
+CTAGAACACCACGTCATCGTCGTTCAGTTCACGCGTCGGTTTGAATTCTTTATTGTCGTGCCACTTCACACCTTTACGCAGATGGAAGGTATAGGTTTTACCGTCTTCGCTGACTTCCCACTTTTCAGCGAGGCCCGGTTTCACTTCATTGGTGCCGTTTTTAAATTCAACCAGGCGGTTTTTAAGCGGTACGGAAGAGTCTTCATAGTTGTTTCCGGAGGTAATCAGCTTCGGTTCTTTCTCTTTTTCA
++
+111111@1>>1>1AA1BF10A0AEE13DGE2A000AA//ABE/11DFFFGG2DE1GE/B//>1BFFE2B21?GGHBF/>///B11010/B1B221BFGFED1/F<FFE//E//BGG><C1BGHHHD22>////<////-.<111>F111<11=.</-.<<EGA00;;:00:.;..:--9;.C..000--;.9.---99-////9/9///;//--;/-----;///////9//-----9/:///;B/9///
+@SRR6244075.2/2
+TTTTATTCTCGTTTGCGAATTACCAGGTGCAGAACGTCGGCCAGCGATACGCGTTAATCCATTCGAAATCCATCGCCGATGAACTGATGACCGGGTGTACAAATTTTGCGTTCAGCGGAAAACCTGGTACCGGGTAGATTCACTTAGCTGCAGCTATCGGGTATCGCCTGCTGAAAGACGGTCAGACAGTGTTTGTGGTTACCGTGGCTGTTGTTATTAGCGCCCTGCACGCCATCTATTACGTCGGGCTT
++
+1>111B33@31>FF11110AA11A110B111110A00A//A///A//B/A/A/>>//2@B1222220/BB11BB//>//>/11>F11B12BB///?/>12211BFGG21/CC<12>/////00?>00>11<.--.<.00==0=DH00<00////;0;/.--.-:9.9.9.9C00000/9..C../09//;//;;/;--:A//B-;---9--;/BE/9////---99---/-----/9/;///---------
diff -r 000000000000 -r 6325216db1fe test-data/reverse_unmapped.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reverse_unmapped.fastq	Wed Dec 06 10:26:15 2017 -0500
@@ -0,0 +1,8 @@
+@SRR6244075.13/2
+TTATTAATTTGATTGTGTTTACTGACGGTGAACGTATTCTAGGTCTTGGTGACCATGTCATCTTCGGTTTTTTCCTTTTTTTTTTTTTACTTTTTCTTTTTTCCCCCTTTTTTGGCTTCCTCCCCTTGTTTTTCCTTTTTTTTTTTCTTTATTTTTGTACTCATCACCCTCAGCTTCTTTTCTTTCCTCTTTTTTTTGTTCTGCGTAATTCTCTGTTCTCTTTCTCCTTTTTCTTTTTTTTTTTTGTTTTT
++
+1>1>>3333@33BB1B31B131B33B00A00110A0DF2D22111DF11A/11A111222DD222//A/A///011D211/>///>>//11>>110>1>>1/0110//0111///11001110//00011>0.0<1<111------/090090000-9;00090000/....9/0000090000///////9/;-@-9--/9//-9---//;B/:;9//////9//////:/99/9;9=-;9--;-:-9--
+@SRR6244075.21/2
+TCGTCGCATCCTGAATGCGCAACAGATTAGCCTGCAATTTGTCGCCTGCCGCTTCCAGCGTATCCTGCAATTCACGCAGCGTCCCGGAAGTTTCCGAAAGCAACAATTCACAGCTGGAAATCGCCGCCCGCCAGTCTTTGTTCAGCAACTGGGCGATATCGTCCTTCACCTGCTGCTGCTGTTCGTCCATCAGACGTTGCGTCAGGTCGATACTGTCGAAAATTTCTGCTACCGAATATTTCAGTGGCG
++
+>>3AA@D2A@FFCB4FGFAECEECF3GHC3FGGAGGFGHH5GGEHDGHHF?EEGEGEEGCFFGFHHHHFFGHGBEAG?EEEGGEFGGGCDGHHHHFGDCGGGFFFHHHHFHFHHHHGEFFGHGEGCCDCDGGGGHHHHHFHHHBFHHBGHHBAGGCGDGHGHFGGGGGGFFGGGGGGGFGGGGGDGGGBFGFF0F=EFFD?FBFF.FFB-A.@FFFFFEA.9FFFFFFFFFFF?B9A.FFFFFBBFBA9