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mapQfilter_wrapper.xml test-data/inputMapqfilter.bam test-data/outputMapqfilter.bam tool_dependencies.xml |
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| diff -r 000000000000 -r 74980f9f1ccc mapQfilter_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mapQfilter_wrapper.xml Tue Nov 10 08:32:58 2015 -0500 |
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| b'@@ -0,0 +1,83 @@\n+<tool id="mapQfilter" name="mapQfilter" version="1.0">\n+ <description>Filters reads on quality, and remove both members of the pair</description>\n+ <requirements>\n+\t<requirement type="package" version="0.1.19">samtools</requirement>\n+ <requirement type="package" version="1.136">picard</requirement>\n+ </requirements> \n+ <command>\n+\t\tsamtools view -b -h -f 0x2 -F 0x100 -o tmpBAM.BAM -q $mapQ $input1\n+\t\t&& \n+\t\tsamtools view tmpBAM.BAM | cut -f 1 | sort | uniq -c | grep \' 1 \' | cut -f8 -d \' \' > min30.list \n+\t\t&& \n+\t\tjava -jar \\$JAVA_JAR_PATH/picard.jar FilterSamReads I=tmpBAM.BAM FILTER=excludeReadList RLF=min30.list OUTPUT="${output1}" VALIDATION_STRINGENCY=LENIENT QUIET=true VERBOSITY=ERROR\n+\t</command>\n+ <inputs>\n+ <param name="input1" type="data" format="bam" label="BAM File to filter"/>\n+ <param name="mapQ" type="integer" value="30" label="Remove pairs with at least one read under the mapping quality of"/>\n+ </inputs>\n+ <outputs>\n+ <data format="bam" name="output1" label="${tool.name} on ${on_string} (bam)"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input1" value="inputMapqfilter.bam" />\n+ <param name="mapQ" value="41" />\n+ <output name="output1" file="outputMapqfilter.bam" ftype="bam" />\n+\t</test>\n+ </tests>\n+ <help><![CDATA[\n+**Filters paired end reads on quality, properly paired and not secondary alignment status, and remove both members of the pair**\n+\n+-----\n+\n+**what it does :**\n+\n+This tool filters out secondary alignments and not properly paired read pairs. You can also define a threshold to filters out read pairs with at least one of the member is below the threshold.\n+It uses samtools and picard tools. The aim of this program is to avoid singleton when you filter with samtools filter on mapq value. If only on member of the read pair is below the threshold, the non-filtered read is kept and become a singleton.\n+MapQFilter provides a bam file with filtered read pairs. \n+-----\n+\n+**input and output formats :**\n+\n+input format: bam file\n+output format: bam file\n+\n+-----\n+\n+**example :**\n+\n+input bam (sam):\n+----------------\n+\n+HWI-D00381:238:C5V3UANXX:4:1101:10239:22220\t99\tContig_20\t437303\t60\t100M\t=\t437511\t308\tAGTAATCCGGCTTGTCATCGAAGCGGAGGGAACGAGTGTAATTGAGGTAGATGGCGAACTCGTTGGGGAAGCCACGGCAGAGCACCTCGGTGGGCGTCGT\tBCCCBGGGGGGGGGFGFGGGFGGGGGBEBGGGGGGGFGGGFGGGGGGGGGGEGGGGGDGEGGGBFBGGGGGGGEGGGGGGGGGGGEGGGGCGGGGGGGDC\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\n+HWI-D00381:238:C5V3UANXX:4:1101:10239:22220\t147\tContig_20\t437511\t60\t100M\t=\t437303\t-308\tCTCCATGTCGTCACGGCGGGATTGTTCTAGTCAAGTAAGCTACTGCACATCATTTGCAATCGGGCTACTTACCGACACCCAGGTGAGTGTTGATACTGGC\tGCDGGGGFGGGDGAGGGGGGGGEFFGGGGGGGGGGGGGCEGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\n+HWI-D00381:238:C5V3UANXX:4:1101:12349:79395\t401\tContig_20\t731638\t1\t68H32M\tContig_22\t594669\t0\tAATGTTATGGACTGGCCTTAAGGGAGAATGCA\tGGGGGGGGGGGGGBGGGGGGGGGGGGGBCBBB\tNM:i:0\tMD:Z:32\tAS:i:32\tXS:i:31\tSA:Z:Contig_22,287814,-,70M30S,6,0;\tXA:Z:Contig_22,+275079,31M69S,0;Contig_20,+766449,31M69S,0;\n+HWI-D00381:238:C5V3UANXX:4:1101:12643:50485\t65\tContig_20\t753418\t5\t73M27S\tContig_22\t309172\t0\tTTGTAGTAGATACAATCCAATAATCTATCTCCCAAATCATTCCTAACCTTAGTGATCCAATTTTCCACAATTAAGTATTTAACTATTTAGTAGAGTAGTA\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGBGGGGDGGGG\tNM:i:3\tMD:Z:1C23C6T40\tAS:i:61\tXS:i:57\tSA:Z:Contig_22,628627,+,69S31M,0,0;\tXA:Z:Contig_20,+746712,69M31S,3;Contig_22,+202567,69M31S,3;Contig_22,+170906,69M31S,4;\n+HWI-D00381:238:C5V3UANXX:4:1101:1493:2084\t99\tContig_22\t181831\t38\t100M\t=\t181974\t250\tTTACTTGCTTAAGCGCAAGGAGCTCTGCCTTAGTAGTTAACGTGGTAATAGTTGCTTGTTAAGCTGCCTTCTAAATAATAGGTCCTCTAAAGAGCGTAAT\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:85\tXA:Z:Contig_20,-721023,100M,3;Contig_20,-731502,100M,4;\n+HWI-D00381:238:C5V3UANXX:4:1'..b'GGGGGGGGGGGGGGGGGCCBB@\tNM:i:7\tMD:Z:74^GGTTTAG26\tAS:i:87\tXS:i:100\n+HWI-D00381:238:C5V3UANXX:4:1101:12349:79395\t145\tContig_22\t287814\t6\t70M30S\t=\t594669\t306787\tCTAAATTATAGTCTAATACTACTAACTATAAAATTCTTATACCCTTAGTAATTCCCTAGGTATATTGCAATGTTATGGACTGGCCTTAAGGGAGAATGCA\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGBGGGGGGGGGGGGGBCBBB\tNM:i:0\tMD:Z:70\tAS:i:70\tXS:i:66\tSA:Z:Contig_20,731638,-,68S32M,1,0;\tXA:Z:Contig_22,+664888,34S66M,0;Contig_20,+998169,34S66M,0;Contig_20,+734056,34S66M,0;Contig_22,+501074,30S70M,2;\n+HWI-D00381:238:C5V3UANXX:4:1101:12643:50485\t129\tContig_22\t309172\t19\t5S95M\tContig_20\t753418\t0\tAACACAAGAATAATACTTGTCTTTTCTAAGCCCTGCGCGAAGCGCAGGTTTTGCACAGCTTAGGCGCCAAGACACTAAACCTAGCTAGGGATGCACCTAA\tBCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\tNM:i:3\tMD:Z:19C8C64G1\tAS:i:83\tXS:i:75\tXA:Z:Contig_22,+398438,100M,5;Contig_22,+302850,100M,6;Contig_20,-126891,100M,6;Contig_22,+586639,100M,6;\n+HWI-D00381:238:C5V3UANXX:4:1101:10799:65426\t163\tContig_22\t318408\t60\t100M\t=\t318624\t316\tCACTTAGCTAGGTTTTAGGTAGTTTCTTAAACTATAGCCTTAAACTACTTAATATCCTTCTAATAGGTAACTATAGCTTCCTTCTCCTTATCCCCTTTAG\tBCBBCGGFGGGGGGGGGGGGFGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGFGGGGGGGGGGGGGGGGCGGGGGDG\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:50\n+HWI-D00381:238:C5V3UANXX:4:1101:10799:65426\t83\tContig_22\t318624\t40\t100M\t=\t318408\t-316\tTACTTACTAGATTGCAATACTTATTCTAGGAGATACAGTACTAGCACTTCTTAGAATTCTTTAACTTAAAATTAAAATTATTAAACCTACCCCTAGCTAG\tGGGGGGGFGFGGGGGGGGGGGFGCBGGGGEGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGFBGGGGGGGGGGCCCCC\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:100\n+HWI-D00381:238:C5V3UANXX:4:1101:14972:98916\t99\tContig_22\t349821\t39\t97M\t=\t349999\t274\tTATAGGCGCGCGAGTAGGTAGTAGGGGCAAGCAGAGTAATAGTATTATTAGTTTAAGCCCTTAATATAAGATCCTTAAAATAATAGTAGAGCTAGTA\tABB@AC1E/E/9B9C>1<1EFGGGG//E>GGBFFEG<F:CF1CGGD1<FFF=<B>11E@@GG1CCFCFFG@@GG0D@>EGC0FG0;=@G@@0<FGFG\tNM:i:0\tMD:Z:97\tAS:i:97\tXS:i:82\tXA:Z:Contig_22,+619968,97M,3;\n+HWI-D00381:238:C5V3UANXX:4:1101:14972:98916\t147\tContig_22\t349999\t9\t96M4S\t=\t349821\t-274\tAAGGTGATCCTCCTAGTAACTATAATAAAACTAAAGCTAGTTGCAGAGGGCTTAGTAGACGTTAGGATTATTAGCAAGTATAGCCTCTAACCTAGTATAG\tGF0FBGF<BF0CECG>CGGCGGG>GGGF1=G>E1GGGF@GFFC@:C1BB@GFFFE>GFFGGFGCFBCCGBC@1BFEF1FGGGGGE1GGGGGGGB>ABBBA\tNM:i:7\tMD:Z:0G4A36A0T9G1C21A18\tAS:i:65\tXS:i:80\n+HWI-D00381:238:C5V3UANXX:4:1101:12349:79395\t97\tContig_22\t594669\t0\t100M\t=\t287814\t-306787\tATTAGGGTCCTTAATTTAGCAACCCTACTATAACTAAACCTAAGATAATAGAGATACAGGTAGGATATAGGCGTCTCCTGCTCTCTTATACTACTATATT\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\tNM:i:3\tMD:Z:6A1T47T43\tAS:i:86\tXS:i:85\n+HWI-D00381:238:C5V3UANXX:4:1101:12643:50485\t321\tContig_22\t628627\t0\t69H31M\t=\t309172\t-319456\tATTAAGTATTTAACTATTTAGTAGAGTAGTA\tFGGGGGGGGGGGGGGGGGGGGBGGGGDGGGG\tNM:i:0\tMD:Z:31\tAS:i:31\tXS:i:31\tSA:Z:Contig_20,753418,+,73M27S,5,3;\tXA:Z:Contig_20,-60185,31M69S,0;Contig_20,-657698,31M69S,0;\n+\n+\n+output bam (sam):\n+-----------------\n+\n+HWI-D00381:238:C5V3UANXX:4:1101:10239:22220\t99\tContig_20\t437303\t60\t100M\t=\t437511\t308\tAGTAATCCGGCTTGTCATCGAAGCGGAGGGAACGAGTGTAATTGAGGTAGATGGCGAACTCGTTGGGGAAGCCACGGCAGAGCACCTCGGTGGGCGTCGT\tBCCCBGGGGGGGGGFGFGGGFGGGGGBEBGGGGGGGFGGGFGGGGGGGGGGEGGGGGDGEGGGBFBGGGGGGGEGGGGGGGGGGGEGGGGCGGGGGGGDC\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\n+HWI-D00381:238:C5V3UANXX:4:1101:10239:22220\t147\tContig_20\t437511\t60\t100M\t=\t437303\t-308\tCTCCATGTCGTCACGGCGGGATTGTTCTAGTCAAGTAAGCTACTGCACATCATTTGCAATCGGGCTACTTACCGACACCCAGGTGAGTGTTGATACTGGC\tGCDGGGGFGGGDGAGGGGGGGGEFFGGGGGGGGGGGGGCEGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\n+\n+-----\n+\n+**reference :**\n+Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]\n+samtools: http://www.htslib.org/\n+picard tools: http://broadinstitute.github.io/picard/\n+\n+]]>\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r 74980f9f1ccc tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Nov 10 08:32:58 2015 -0500 |
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| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="picard" version="1.136"> + <repository changeset_revision="3e9c24e5325b" name="package_picard_1_136" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |