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Changeset 0:12f2a7545ff2 (2017-10-16)

Next changeset 1:d6c27ab8d084 (2017-10-16)

Commit message:
Uploaded

added:
01_RemoveSNPs/RemoveSNPs
01_RemoveSNPs/RemoveSNPs.xml
01_RemoveSNPs/input.sam
01_RemoveSNPs/output.sam
01_RemoveSNPs/test-data/input.sam
01_RemoveSNPs/test-data/output.sam
01_RemoveSNPs/test.xml
01_RemoveSNPs/tool_build.sh

diff -r 000000000000 -r 12f2a7545ff2 01_RemoveSNPs/RemoveSNPs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/01_RemoveSNPs/RemoveSNPs Mon Oct 16 13:59:28 2017 -0400

[

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+#if [ "$1" == "-h" ]; then
+if [[ -z $1 || -z $2 || $1 == "-h" ]]; then
+    echo "This program will remove mismatches from sam file."
+    echo "Usage: `basename $0` test.sam 3"
+    exit 0
+fi
+
+cmd="echo perl -ne 'print if((/XM:i:[0-$2][^0-9]/) || (/^@/));' $1"
+eval `$cmd`
\ No newline at end of file

diff -r 000000000000 -r 12f2a7545ff2 01_RemoveSNPs/RemoveSNPs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/01_RemoveSNPs/RemoveSNPs.xml Mon Oct 16 13:59:28 2017 -0400

[

@@ -0,0 +1,34 @@
+<tool id="RemoveSNPs" name="Remove Mismatches (SNPs) from SAM Alignment file" version="0.1.0">
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        bash $__tool_directory__/RemoveSNPs "$input1" 3 > "$output1"
+    ]]></command>
+    <inputs>
+        <param type="data" name="SAM alignment files" format="sam" />
+ <param type="integer" name="SNPs/ mismatches allowed" value="3" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="sam" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="input.sam"/>
+            <output name="output1" file="output.sam"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This program will remove mismatches from sam file.\n Usage: RemoveSNPs test.sam 3
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{RemoveSNPs,
+  author = {Tanwar, Deepak},
+  year = {2017},
+  title = {RemoveSNPs},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/dktanwar/NGS_Sperm_H3K4me3_Planemo_tools/tree/master/01_RemoveSNPs},
+}</citation>
+    </citations>
+</tool>

diff -r 000000000000 -r 12f2a7545ff2 01_RemoveSNPs/input.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/01_RemoveSNPs/input.sam Mon Oct 16 13:59:28 2017 -0400

b'@@ -0,0 +1,1000 @@\n+@HD\tVN:1.0\tSO:unsorted\n+@SQ\tSN:chr1\tLN:249250621\n+@SQ\tSN:chr2\tLN:243199373\n+@SQ\tSN:chr3\tLN:198022430\n+@SQ\tSN:chr4\tLN:191154276\n+@SQ\tSN:chr5\tLN:180915260\n+@SQ\tSN:chr6\tLN:171115067\n+@SQ\tSN:chr7\tLN:159138663\n+@SQ\tSN:chrX\tLN:155270560\n+@SQ\tSN:chr8\tLN:146364022\n+@SQ\tSN:chr9\tLN:141213431\n+@SQ\tSN:chr10\tLN:135534747\n+@SQ\tSN:chr11\tLN:135006516\n+@SQ\tSN:chr12\tLN:133851895\n+@SQ\tSN:chr13\tLN:115169878\n+@SQ\tSN:chr14\tLN:107349540\n+@SQ\tSN:chr15\tLN:102531392\n+@SQ\tSN:chr16\tLN:90354753\n+@SQ\tSN:chr17\tLN:81195210\n+@SQ\tSN:chr18\tLN:78077248\n+@SQ\tSN:chr20\tLN:63025520\n+@SQ\tSN:chrY\tLN:59373566\n+@SQ\tSN:chr19\tLN:59128983\n+@SQ\tSN:chr22\tLN:51304566\n+@SQ\tSN:chr21\tLN:48129895\n+@SQ\tSN:chr6_ssto_hap7\tLN:4928567\n+@SQ\tSN:chr6_mcf_hap5\tLN:4833398\n+@SQ\tSN:chr6_cox_hap2\tLN:4795371\n+@SQ\tSN:chr6_mann_hap4\tLN:4683263\n+@SQ\tSN:chr6_apd_hap1\tLN:4622290\n+@SQ\tSN:chr6_qbl_hap6\tLN:4611984\n+@SQ\tSN:chr6_dbb_hap3\tLN:4610396\n+@SQ\tSN:chr17_ctg5_hap1\tLN:1680828\n+@SQ\tSN:chr4_ctg9_hap1\tLN:590426\n+@SQ\tSN:chr1_gl000192_random\tLN:547496\n+@SQ\tSN:chrUn_gl000225\tLN:211173\n+@SQ\tSN:chr4_gl000194_random\tLN:191469\n+@SQ\tSN:chr4_gl000193_random\tLN:189789\n+@SQ\tSN:chr9_gl000200_random\tLN:187035\n+@SQ\tSN:chrUn_gl000222\tLN:186861\n+@SQ\tSN:chrUn_gl000212\tLN:186858\n+@SQ\tSN:chr7_gl000195_random\tLN:182896\n+@SQ\tSN:chrUn_gl000223\tLN:180455\n+@SQ\tSN:chrUn_gl000224\tLN:179693\n+@SQ\tSN:chrUn_gl000219\tLN:179198\n+@SQ\tSN:chr17_gl000205_random\tLN:174588\n+@SQ\tSN:chrUn_gl000215\tLN:172545\n+@SQ\tSN:chrUn_gl000216\tLN:172294\n+@SQ\tSN:chrUn_gl000217\tLN:172149\n+@SQ\tSN:chr9_gl000199_random\tLN:169874\n+@SQ\tSN:chrUn_gl000211\tLN:166566\n+@SQ\tSN:chrUn_gl000213\tLN:164239\n+@SQ\tSN:chrUn_gl000220\tLN:161802\n+@SQ\tSN:chrUn_gl000218\tLN:161147\n+@SQ\tSN:chr19_gl000209_random\tLN:159169\n+@SQ\tSN:chrUn_gl000221\tLN:155397\n+@SQ\tSN:chrUn_gl000214\tLN:137718\n+@SQ\tSN:chrUn_gl000228\tLN:129120\n+@SQ\tSN:chrUn_gl000227\tLN:128374\n+@SQ\tSN:chr1_gl000191_random\tLN:106433\n+@SQ\tSN:chr19_gl000208_random\tLN:92689\n+@SQ\tSN:chr9_gl000198_random\tLN:90085\n+@SQ\tSN:chr17_gl000204_random\tLN:81310\n+@SQ\tSN:chrUn_gl000233\tLN:45941\n+@SQ\tSN:chrUn_gl000237\tLN:45867\n+@SQ\tSN:chrUn_gl000230\tLN:43691\n+@SQ\tSN:chrUn_gl000242\tLN:43523\n+@SQ\tSN:chrUn_gl000243\tLN:43341\n+@SQ\tSN:chrUn_gl000241\tLN:42152\n+@SQ\tSN:chrUn_gl000236\tLN:41934\n+@SQ\tSN:chrUn_gl000240\tLN:41933\n+@SQ\tSN:chr17_gl000206_random\tLN:41001\n+@SQ\tSN:chrUn_gl000232\tLN:40652\n+@SQ\tSN:chrUn_gl000234\tLN:40531\n+@SQ\tSN:chr11_gl000202_random\tLN:40103\n+@SQ\tSN:chrUn_gl000238\tLN:39939\n+@SQ\tSN:chrUn_gl000244\tLN:39929\n+@SQ\tSN:chrUn_gl000248\tLN:39786\n+@SQ\tSN:chr8_gl000196_random\tLN:38914\n+@SQ\tSN:chrUn_gl000249\tLN:38502\n+@SQ\tSN:chrUn_gl000246\tLN:38154\n+@SQ\tSN:chr17_gl000203_random\tLN:37498\n+@SQ\tSN:chr8_gl000197_random\tLN:37175\n+@SQ\tSN:chrUn_gl000245\tLN:36651\n+@SQ\tSN:chrUn_gl000247\tLN:36422\n+@SQ\tSN:chr9_gl000201_random\tLN:36148\n+@SQ\tSN:chrUn_gl000235\tLN:34474\n+@SQ\tSN:chrUn_gl000239\tLN:33824\n+@SQ\tSN:chr21_gl000210_random\tLN:27682\n+@SQ\tSN:chrUn_gl000231\tLN:27386\n+@SQ\tSN:chrUn_gl000229\tLN:19913\n+@SQ\tSN:chrM\tLN:16571\n+@SQ\tSN:chrUn_gl000226\tLN:15008\n+@SQ\tSN:chr18_gl000207_random\tLN:4262\n+@PG\tID:bowtie2\tPN:bowtie2\tVN:2.2.9\tCL:"/Volumes/BINF1_Raid/share/apps/bowtie2-2.2.9/bowtie2-align-s --wrapper basic-0 -x ../../../data/genomes/homo_sapiens/ucsc/hg19_bowtie/hg19 -S output/HI.3700.003.Index_19.RCS_375-Post_gradient-ChIP.sam -p 5 -q /dev/fd/63"\n+SN916:366:C8YJTACXX:3:1112:13199:26910\t0\tchrX\t155260311\t1\t84M\t*\t0\t0\tAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\t=+??++2A?DCDDF@BCE?FFGCFFFIF:E=FFE*:?B;F??FECBB;CADF@A((.=.===)=.;;((...(5?2-,5(9<5?\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:84\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2114:10500:26116\t0\tchr5\t10505\t1\t100M\t*\t0\t0\tTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC\tCCCFFFFFHHHHHJJJIJJJJJIIJJJJJIJJJJJJIIJJIJJJJJJJJJJJJJJIJJJJHGHHFFFFFEEDCDD?ABDDDDDDDDCDDDBDCADDDDDB\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:1309:11800:96899\t0\tchr5\t11034\t1\t100M\t*\t0'..b'6:C8YJTACXX:3:2202:15692:96741\t0\tchr1\t80479\t1\t100M\t*\t0\t0\tCTGAAAGCCTTCTGCACATCAAAATAAATAATCAGCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCACAAACTATGCATCCAACAGAGGAC\tCCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJJJJJJJJJGHIJJJJJJJJJJJJJJJJIFGIJJIJJHHHHHHF@DEFEDEEEEDEEDDDDDDDDDDDD\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2312:11477:30607\t16\tchr6\t70713\t1\t100M\t*\t0\t0\tAACTGTTTCCAAGTTACAATGGTTCAACCATTTTTCAGCTTTATGGTGGTGTGAAAGTGATATCCATTCATTAGAAACCATGCTCCAGGATGGGCGCAGT\tDDDDDDDDDDEEDEEDDEEEDEFEBFFHHHHHIIIJJJJIGJJJIJJIIJJJJJJJJJJJIJJJJJJIJJJJJJJIGJJJJJJIJJJHHHHHFFFFFC@@\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2102:15892:55875\t0\tchr1\t80923\t1\t100M\t*\t0\t0\tATACAAAAATTAGCTGGGCATTGTGGTGCGTGCCTGTAATCCCAGCTATTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCAGGGAGTCGGAGGTGTTG\tCCCFFFFFHHHHHJJJJJJJJJJHIJGHJJHIJJIJIJJJJJJJJJIGIJJJIJIJJJIHHHGFFFDD?BDCCDDCDDCDDDDDDDBD<CBD9BD(8:?A\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2210:19963:85931\t16\tchr1\t81348\t6\t99M\t*\t0\t0\tATTAGTCCCATCATTCAGCAATTAACTTTAGCTCAATGCTTCAAAAATTCTTCAGGCCCTGTGTAATTTCAGCTACGTACATTAATGATGAGTACCCAT\tCCCBBC?EECEEEECFB:>DHE?7CAAEC>GIIIIIIIHCGFEDB99GIGHHCHD;@EFGGGGIIIHFFGFHFC;GGFAH@GGHBEDDBFFDDFDD@@@\tAS:i:0\tXS:i:-5\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:99\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:1206:20394:64940\t0\tchr6\t71557\t1\t100M\t*\t0\t0\tTGTTCTGAGCATGTTCAAAGTAAGCTAGGCCAACCTATAATTTTCGGTGTGCTAAATGCATTTTTAACTTATGATATTTTCAGTTTACGGGGGTTTGTTG\tCCCFFFFFHHHHHHIJJJJJHIJJJJJJIIJJJJJJJJJJJIJJJIJIIIJJIJJJJIJJIJJJIJJIJJJJJJHAHHHHHHFFFFFFCCCDD9@DDDDB\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:1114:18197:77218\t16\tchr1\t587720\t1\t100M\t*\t0\t0\tCCTAGGCTCACAGCAAGAAAAAATGAAGGCTAAGGCAGAATTATATATGGCTCCGCTAAGTGTTGAGGGAGCCCCAATACAGAGTCAGTAAGCAAAGTCT\tCDDDDDCCDDDDDDDDDDCEDEECCEEFFECFDE@HHHHHIIJJJIHGIGHGGJIJJJJIIIIHHEHGHIGBBJJJJHHJIJJHGIIHHHFHFFFFF@CB\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2305:7747:95151\t0\tchr1\t81656\t6\t100M\t*\t0\t0\tTGAGACATAACTTCATCATACATCAAGGAGCATCTGTATATGGGATATAGTTAAAGCAGTGATCAGAGGAAAATCTATAGCCTTAACACATTTATTAATA\tCCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJJJJJIJGIJJJJJJJJJJJJJJCGIJJGHHHGFFFFFFEFEEEEEED\tAS:i:0\tXS:i:-5\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2314:9837:14011\t16\tchr1\t80357\t34\t100M\t*\t0\t0\tAAAATTCTAGAAGATAAGATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCACAATCAAGAACCCAAAAGCAAACACAACAAAACAAAGAT\tDDC@A<DDDDEDDEDEDEECFFDB?FHCHJJGGIGJIHIIIIHEJIIIJIIIFIIGJIHCIIIHFJJIIGEJJIIGIGHGJGGEFJIHHGHHDFEFFCCC\tAS:i:0\tXS:i:-26\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2108:4228:69091\t0\tchr1\t402707\t1\t100M\t*\t0\t0\tCTGCCTTAGCCTTCATTTTTTCTTGCTGTGAGCCTAGGAATTACTAAAGGTGAGTTATTAGTGTCTTCTCAGGCCTTTTCTGAGCATGTGTCCCACCTTG\t@CCFFFFFHHHHHIIIJJJIIJJJFIJJJJIJJJJGGIGIJJJJJJJIJIFDFHJIGIJJJIJJJGIHIJJIIIC=AHHEFFDFDFEEEEFEDDDDDDDA\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:1114:9198:9903\t16\tchr19\t124922\t1\t96M\t*\t0\t0\tCAGGAAGACTATTTGAAGAAATGTGTTTGAAAGCTTCCCAAATTTCACTAAAAACAAATATATACATTCAAAAAGCTCAGTGAACTTCATCAAGGA\tAA@>3ADEDDDDDCCAA?A?=6;C3;CAF;FB2B=@BGFB<?GB*9DDG@;?;?FFECC9?91*EB<A<E?A<A<BFEG<EA+,8F>BD>D=B<7@\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:96\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2312:18422:64139\t0\tchr5\t180827216\t1\t100M\t*\t0\t0\tAGAGTTTAATTCATTTGTATTTAATGTAATTACTGATAAAGAGGGGCTTACTCCTACCATTTTGCTTTTGTTTTCTGTATGTCTTATACCTCCTTTGTTC\t??7D=ADDBHHHDHIIIC@HEGFGDHIIIIFIIIGIGIBHGEIHDBEIFIIIIIIGGIIEE@GEG=@FGCCDA>CCE=CHH=ACEEEEEECCCCC@CACC\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:1109:11043:55419\t0\tchr1\t84444\t6\t100M\t*\t0\t0\tTGGTAACCACTAAGTTAATATCTTTTGAAAATACAGAAAAGGAAAGCACAGGGTAAACACAGTGATATGCTACAAAATAGCAACTAAACACAAAAGAAGG\t@@@BDDDDFFDHFEFHB<C@?:ACCDEHIGGHC??F>FGAFDEC?@@BBDGB;D9DB8CEIAEGA;47CC4.=;77.=7?CEC;BCC:>>?;;5=>8?:?\tAS:i:0\tXS:i:-5\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n'

diff -r 000000000000 -r 12f2a7545ff2 01_RemoveSNPs/output.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/01_RemoveSNPs/output.sam Mon Oct 16 13:59:28 2017 -0400

b'@@ -0,0 +1,959 @@\n+@HD\tVN:1.0\tSO:unsorted\n+@SQ\tSN:chr1\tLN:249250621\n+@SQ\tSN:chr2\tLN:243199373\n+@SQ\tSN:chr3\tLN:198022430\n+@SQ\tSN:chr4\tLN:191154276\n+@SQ\tSN:chr5\tLN:180915260\n+@SQ\tSN:chr6\tLN:171115067\n+@SQ\tSN:chr7\tLN:159138663\n+@SQ\tSN:chrX\tLN:155270560\n+@SQ\tSN:chr8\tLN:146364022\n+@SQ\tSN:chr9\tLN:141213431\n+@SQ\tSN:chr10\tLN:135534747\n+@SQ\tSN:chr11\tLN:135006516\n+@SQ\tSN:chr12\tLN:133851895\n+@SQ\tSN:chr13\tLN:115169878\n+@SQ\tSN:chr14\tLN:107349540\n+@SQ\tSN:chr15\tLN:102531392\n+@SQ\tSN:chr16\tLN:90354753\n+@SQ\tSN:chr17\tLN:81195210\n+@SQ\tSN:chr18\tLN:78077248\n+@SQ\tSN:chr20\tLN:63025520\n+@SQ\tSN:chrY\tLN:59373566\n+@SQ\tSN:chr19\tLN:59128983\n+@SQ\tSN:chr22\tLN:51304566\n+@SQ\tSN:chr21\tLN:48129895\n+@SQ\tSN:chr6_ssto_hap7\tLN:4928567\n+@SQ\tSN:chr6_mcf_hap5\tLN:4833398\n+@SQ\tSN:chr6_cox_hap2\tLN:4795371\n+@SQ\tSN:chr6_mann_hap4\tLN:4683263\n+@SQ\tSN:chr6_apd_hap1\tLN:4622290\n+@SQ\tSN:chr6_qbl_hap6\tLN:4611984\n+@SQ\tSN:chr6_dbb_hap3\tLN:4610396\n+@SQ\tSN:chr17_ctg5_hap1\tLN:1680828\n+@SQ\tSN:chr4_ctg9_hap1\tLN:590426\n+@SQ\tSN:chr1_gl000192_random\tLN:547496\n+@SQ\tSN:chrUn_gl000225\tLN:211173\n+@SQ\tSN:chr4_gl000194_random\tLN:191469\n+@SQ\tSN:chr4_gl000193_random\tLN:189789\n+@SQ\tSN:chr9_gl000200_random\tLN:187035\n+@SQ\tSN:chrUn_gl000222\tLN:186861\n+@SQ\tSN:chrUn_gl000212\tLN:186858\n+@SQ\tSN:chr7_gl000195_random\tLN:182896\n+@SQ\tSN:chrUn_gl000223\tLN:180455\n+@SQ\tSN:chrUn_gl000224\tLN:179693\n+@SQ\tSN:chrUn_gl000219\tLN:179198\n+@SQ\tSN:chr17_gl000205_random\tLN:174588\n+@SQ\tSN:chrUn_gl000215\tLN:172545\n+@SQ\tSN:chrUn_gl000216\tLN:172294\n+@SQ\tSN:chrUn_gl000217\tLN:172149\n+@SQ\tSN:chr9_gl000199_random\tLN:169874\n+@SQ\tSN:chrUn_gl000211\tLN:166566\n+@SQ\tSN:chrUn_gl000213\tLN:164239\n+@SQ\tSN:chrUn_gl000220\tLN:161802\n+@SQ\tSN:chrUn_gl000218\tLN:161147\n+@SQ\tSN:chr19_gl000209_random\tLN:159169\n+@SQ\tSN:chrUn_gl000221\tLN:155397\n+@SQ\tSN:chrUn_gl000214\tLN:137718\n+@SQ\tSN:chrUn_gl000228\tLN:129120\n+@SQ\tSN:chrUn_gl000227\tLN:128374\n+@SQ\tSN:chr1_gl000191_random\tLN:106433\n+@SQ\tSN:chr19_gl000208_random\tLN:92689\n+@SQ\tSN:chr9_gl000198_random\tLN:90085\n+@SQ\tSN:chr17_gl000204_random\tLN:81310\n+@SQ\tSN:chrUn_gl000233\tLN:45941\n+@SQ\tSN:chrUn_gl000237\tLN:45867\n+@SQ\tSN:chrUn_gl000230\tLN:43691\n+@SQ\tSN:chrUn_gl000242\tLN:43523\n+@SQ\tSN:chrUn_gl000243\tLN:43341\n+@SQ\tSN:chrUn_gl000241\tLN:42152\n+@SQ\tSN:chrUn_gl000236\tLN:41934\n+@SQ\tSN:chrUn_gl000240\tLN:41933\n+@SQ\tSN:chr17_gl000206_random\tLN:41001\n+@SQ\tSN:chrUn_gl000232\tLN:40652\n+@SQ\tSN:chrUn_gl000234\tLN:40531\n+@SQ\tSN:chr11_gl000202_random\tLN:40103\n+@SQ\tSN:chrUn_gl000238\tLN:39939\n+@SQ\tSN:chrUn_gl000244\tLN:39929\n+@SQ\tSN:chrUn_gl000248\tLN:39786\n+@SQ\tSN:chr8_gl000196_random\tLN:38914\n+@SQ\tSN:chrUn_gl000249\tLN:38502\n+@SQ\tSN:chrUn_gl000246\tLN:38154\n+@SQ\tSN:chr17_gl000203_random\tLN:37498\n+@SQ\tSN:chr8_gl000197_random\tLN:37175\n+@SQ\tSN:chrUn_gl000245\tLN:36651\n+@SQ\tSN:chrUn_gl000247\tLN:36422\n+@SQ\tSN:chr9_gl000201_random\tLN:36148\n+@SQ\tSN:chrUn_gl000235\tLN:34474\n+@SQ\tSN:chrUn_gl000239\tLN:33824\n+@SQ\tSN:chr21_gl000210_random\tLN:27682\n+@SQ\tSN:chrUn_gl000231\tLN:27386\n+@SQ\tSN:chrUn_gl000229\tLN:19913\n+@SQ\tSN:chrM\tLN:16571\n+@SQ\tSN:chrUn_gl000226\tLN:15008\n+@SQ\tSN:chr18_gl000207_random\tLN:4262\n+@PG\tID:bowtie2\tPN:bowtie2\tVN:2.2.9\tCL:"/Volumes/BINF1_Raid/share/apps/bowtie2-2.2.9/bowtie2-align-s --wrapper basic-0 -x ../../../data/genomes/homo_sapiens/ucsc/hg19_bowtie/hg19 -S output/HI.3700.003.Index_19.RCS_375-Post_gradient-ChIP.sam -p 5 -q /dev/fd/63"\n+SN916:366:C8YJTACXX:3:1112:13199:26910\t0\tchrX\t155260311\t1\t84M\t*\t0\t0\tAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\t=+??++2A?DCDDF@BCE?FFGCFFFIF:E=FFE*:?B;F??FECBB;CADF@A((.=.===)=.;;((...(5?2-,5(9<5?\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:84\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2114:10500:26116\t0\tchr5\t10505\t1\t100M\t*\t0\t0\tTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC\tCCCFFFFFHHHHHJJJIJJJJJIIJJJJJIJJJJJJIIJJIJJJJJJJJJJJJJJIJJJJHGHHFFFFFEEDCDD?ABDDDDDDDDCDDDBDCADDDDDB\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:1309:11800:96899\t0\tchr5\t11034\t1\t100M\t*\t0\t'..b'6:C8YJTACXX:3:2202:15692:96741\t0\tchr1\t80479\t1\t100M\t*\t0\t0\tCTGAAAGCCTTCTGCACATCAAAATAAATAATCAGCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCACAAACTATGCATCCAACAGAGGAC\tCCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJJJJJJJJJGHIJJJJJJJJJJJJJJJJIFGIJJIJJHHHHHHF@DEFEDEEEEDEEDDDDDDDDDDDD\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2312:11477:30607\t16\tchr6\t70713\t1\t100M\t*\t0\t0\tAACTGTTTCCAAGTTACAATGGTTCAACCATTTTTCAGCTTTATGGTGGTGTGAAAGTGATATCCATTCATTAGAAACCATGCTCCAGGATGGGCGCAGT\tDDDDDDDDDDEEDEEDDEEEDEFEBFFHHHHHIIIJJJJIGJJJIJJIIJJJJJJJJJJJIJJJJJJIJJJJJJJIGJJJJJJIJJJHHHHHFFFFFC@@\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2102:15892:55875\t0\tchr1\t80923\t1\t100M\t*\t0\t0\tATACAAAAATTAGCTGGGCATTGTGGTGCGTGCCTGTAATCCCAGCTATTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCAGGGAGTCGGAGGTGTTG\tCCCFFFFFHHHHHJJJJJJJJJJHIJGHJJHIJJIJIJJJJJJJJJIGIJJJIJIJJJIHHHGFFFDD?BDCCDDCDDCDDDDDDDBD<CBD9BD(8:?A\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2210:19963:85931\t16\tchr1\t81348\t6\t99M\t*\t0\t0\tATTAGTCCCATCATTCAGCAATTAACTTTAGCTCAATGCTTCAAAAATTCTTCAGGCCCTGTGTAATTTCAGCTACGTACATTAATGATGAGTACCCAT\tCCCBBC?EECEEEECFB:>DHE?7CAAEC>GIIIIIIIHCGFEDB99GIGHHCHD;@EFGGGGIIIHFFGFHFC;GGFAH@GGHBEDDBFFDDFDD@@@\tAS:i:0\tXS:i:-5\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:99\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:1206:20394:64940\t0\tchr6\t71557\t1\t100M\t*\t0\t0\tTGTTCTGAGCATGTTCAAAGTAAGCTAGGCCAACCTATAATTTTCGGTGTGCTAAATGCATTTTTAACTTATGATATTTTCAGTTTACGGGGGTTTGTTG\tCCCFFFFFHHHHHHIJJJJJHIJJJJJJIIJJJJJJJJJJJIJJJIJIIIJJIJJJJIJJIJJJIJJIJJJJJJHAHHHHHHFFFFFFCCCDD9@DDDDB\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:1114:18197:77218\t16\tchr1\t587720\t1\t100M\t*\t0\t0\tCCTAGGCTCACAGCAAGAAAAAATGAAGGCTAAGGCAGAATTATATATGGCTCCGCTAAGTGTTGAGGGAGCCCCAATACAGAGTCAGTAAGCAAAGTCT\tCDDDDDCCDDDDDDDDDDCEDEECCEEFFECFDE@HHHHHIIJJJIHGIGHGGJIJJJJIIIIHHEHGHIGBBJJJJHHJIJJHGIIHHHFHFFFFF@CB\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2305:7747:95151\t0\tchr1\t81656\t6\t100M\t*\t0\t0\tTGAGACATAACTTCATCATACATCAAGGAGCATCTGTATATGGGATATAGTTAAAGCAGTGATCAGAGGAAAATCTATAGCCTTAACACATTTATTAATA\tCCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJJJJJIJGIJJJJJJJJJJJJJJCGIJJGHHHGFFFFFFEFEEEEEED\tAS:i:0\tXS:i:-5\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2314:9837:14011\t16\tchr1\t80357\t34\t100M\t*\t0\t0\tAAAATTCTAGAAGATAAGATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCACAATCAAGAACCCAAAAGCAAACACAACAAAACAAAGAT\tDDC@A<DDDDEDDEDEDEECFFDB?FHCHJJGGIGJIHIIIIHEJIIIJIIIFIIGJIHCIIIHFJJIIGEJJIIGIGHGJGGEFJIHHGHHDFEFFCCC\tAS:i:0\tXS:i:-26\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2108:4228:69091\t0\tchr1\t402707\t1\t100M\t*\t0\t0\tCTGCCTTAGCCTTCATTTTTTCTTGCTGTGAGCCTAGGAATTACTAAAGGTGAGTTATTAGTGTCTTCTCAGGCCTTTTCTGAGCATGTGTCCCACCTTG\t@CCFFFFFHHHHHIIIJJJIIJJJFIJJJJIJJJJGGIGIJJJJJJJIJIFDFHJIGIJJJIJJJGIHIJJIIIC=AHHEFFDFDFEEEEFEDDDDDDDA\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:1114:9198:9903\t16\tchr19\t124922\t1\t96M\t*\t0\t0\tCAGGAAGACTATTTGAAGAAATGTGTTTGAAAGCTTCCCAAATTTCACTAAAAACAAATATATACATTCAAAAAGCTCAGTGAACTTCATCAAGGA\tAA@>3ADEDDDDDCCAA?A?=6;C3;CAF;FB2B=@BGFB<?GB*9DDG@;?;?FFECC9?91*EB<A<E?A<A<BFEG<EA+,8F>BD>D=B<7@\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:96\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:2312:18422:64139\t0\tchr5\t180827216\t1\t100M\t*\t0\t0\tAGAGTTTAATTCATTTGTATTTAATGTAATTACTGATAAAGAGGGGCTTACTCCTACCATTTTGCTTTTGTTTTCTGTATGTCTTATACCTCCTTTGTTC\t??7D=ADDBHHHDHIIIC@HEGFGDHIIIIFIIIGIGIBHGEIHDBEIFIIIIIIGGIIEE@GEG=@FGCCDA>CCE=CHH=ACEEEEEECCCCC@CACC\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+SN916:366:C8YJTACXX:3:1109:11043:55419\t0\tchr1\t84444\t6\t100M\t*\t0\t0\tTGGTAACCACTAAGTTAATATCTTTTGAAAATACAGAAAAGGAAAGCACAGGGTAAACACAGTGATATGCTACAAAATAGCAACTAAACACAAAAGAAGG\t@@@BDDDDFFDHFEFHB<C@?:ACCDEHIGGHC??F>FGAFDEC?@@BBDGB;D9DB8CEIAEGA;47CC4.=;77.=7?CEC;BCC:>>?;;5=>8?:?\tAS:i:0\tXS:i:-5\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n'

diff -r 000000000000 -r 12f2a7545ff2 01_RemoveSNPs/test-data/input.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/01_RemoveSNPs/test-data/input.sam Mon Oct 16 13:59:28 2017 -0400

diff -r 000000000000 -r 12f2a7545ff2 01_RemoveSNPs/test-data/output.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/01_RemoveSNPs/test-data/output.sam Mon Oct 16 13:59:28 2017 -0400

diff -r 000000000000 -r 12f2a7545ff2 01_RemoveSNPs/test.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/01_RemoveSNPs/test.xml Mon Oct 16 13:59:28 2017 -0400

[

@@ -0,0 +1,35 @@
+<tool id="RemoveSNPs" name="Remove Mismatches (SNPs) from SAM Alignment file" version="0.1.0">
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        bash $__tool_directory__/RemoveSNPs "$input1" 3 > "$output1"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="sam" />
+<param type="integer" name="SNPs/ mismatches allowed" value="3" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="sam" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="input.sam"/>
+            <output name="output1" file="output.sam"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This program will remove mismatches from sam file.
+        Usage: RemoveSNPs test.sam 3
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{RemoveSNPs,
+  author = {Tanwar, Deepak},
+  year = {2017},
+  title = {RemoveSNPs},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/dktanwar/NGS_Sperm_H3K4me3_Planemo_tools/tree/master/01_RemoveSNPs},
+}</citation>
+    </citations>
+</tool>

diff -r 000000000000 -r 12f2a7545ff2 01_RemoveSNPs/tool_build.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/01_RemoveSNPs/tool_build.sh Mon Oct 16 13:59:28 2017 -0400

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+planemo tool_init --force \
+                    --id 'RemoveSNPs' \
+                    --name 'Remove Mismatches (SNPs) from SAM" version="0.1.0"' \
+                    --example_command 'RemoveSNPs input.sam 3 > output.sam' \
+                    --example_input input.sam \
+                    --example_output output.sam \
+                    --test_case \
+                    --cite_url 'https://github.com/dktanwar/Galaxy_Tools/tree/master/01_mismatch_removal' \
+                    --help_from_command 'mismatchRemovalSam -h'