details: http://www.bx.psu.edu/hg/galaxy/rev/a2cb4b0ccf6b changeset: 3475:a2cb4b0ccf6b user: Kelly Vincent <kpvincent@bx.psu.edu> date: Wed Mar 03 15:37:43 2010 -0500 description: Updated Bowtie wrapper for new fastqcssanger datatype, and added equCab2 to builds.txt so sam_to_bam and sam_pileup will pass diffstat: test-data/bowtie_in1.fastqcssanger | 4 +++ test-data/bowtie_in1.fastqsanger | 4 --- test-data/bowtie_in3.fastqcssanger | 4 +++ test-data/bowtie_in3.fastqsanger | 4 --- test-data/bowtie_in4.fastqcssanger | 4 +++ test-data/bowtie_in4.fastqsanger | 4 --- tool-data/shared/ucsc/builds.txt | 1 + tools/sr_mapping/bowtie_color_wrapper.xml | 32 +++++++++++++++--------------- 8 files changed, 29 insertions(+), 28 deletions(-) diffs (183 lines): diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in1.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in1.fastqcssanger Wed Mar 03 15:37:43 2010 -0500 @@ -0,0 +1,4 @@ +@869_1532_1255/1 +G2102223311000312223321002 ++ +=;8:?@=?;;9:8;=>;5A?;<8>< diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in1.fastqsanger --- a/test-data/bowtie_in1.fastqsanger Wed Mar 03 15:18:09 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@869_1532_1255/1 -G2102223311000312223321002 -+ -=;8:?@=?;;9:8;=>;5A?;<8>< diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in3.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in3.fastqcssanger Wed Mar 03 15:37:43 2010 -0500 @@ -0,0 +1,4 @@ +@869_1532_1255/1 +G2102223311000312223321002 ++ +=;8:?@=?;;9:8;=>;5A?;<8>< diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in3.fastqsanger --- a/test-data/bowtie_in3.fastqsanger Wed Mar 03 15:18:09 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@869_1532_1255/1 -G2102223311000312223321002 -+ -=;8:?@=?;;9:8;=>;5A?;<8>< diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in4.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in4.fastqcssanger Wed Mar 03 15:37:43 2010 -0500 @@ -0,0 +1,4 @@ +@869_1532_1255/2 +T1301222000112122113330022 ++ +;89<:==5<8>69;8=<9;<>9:=< diff -r f0e32644688b -r a2cb4b0ccf6b test-data/bowtie_in4.fastqsanger --- a/test-data/bowtie_in4.fastqsanger Wed Mar 03 15:18:09 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@869_1532_1255/2 -T1301222000112122113330022 -+ -;89<:==5<8>69;8=<9;<>9:=< diff -r f0e32644688b -r a2cb4b0ccf6b tool-data/shared/ucsc/builds.txt --- a/tool-data/shared/ucsc/builds.txt Wed Mar 03 15:18:09 2010 -0500 +++ b/tool-data/shared/ucsc/builds.txt Wed Mar 03 15:37:43 2010 -0500 @@ -786,6 +786,7 @@ aeroHydr_ATCC7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966 (aeroHydr_ATCC7966) baciAnth_AMES Bacillus anthracis str. Ames (baciAnth_AMES) shewOnei Shewanella oneidensis MR-1 (shewOnei) +equCab2 Horse Sep. 2007 (equCab2) arabidopsis Arabidopsis thaliana TAIR9 arabidopsis_tair8 Arabidopsis thaliana TAIR8 araTha1 Arabidopsis thaliana TAIR7 diff -r f0e32644688b -r a2cb4b0ccf6b tools/sr_mapping/bowtie_color_wrapper.xml --- a/tools/sr_mapping/bowtie_color_wrapper.xml Wed Mar 03 15:18:09 2010 -0500 +++ b/tools/sr_mapping/bowtie_color_wrapper.xml Wed Mar 03 15:37:43 2010 -0500 @@ -210,7 +210,7 @@ <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own"> <option value="indexPreSet">Default</option> <option value="indexFull">Set your own</option> - </param> + </param> <when value="indexPreSet" /> <when value="indexFull"> <conditional name="autoBehavior"> @@ -259,7 +259,7 @@ <option value="paired">Paired-end</option> </param> <when value="single"> - <param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="sInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> <conditional name="sParams"> <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> <option value="preSet">Commonly used</option> @@ -317,8 +317,8 @@ </conditional> <!-- csParams --> </when> <!-- cSingle --> <when value="paired"> - <param name="pInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param name="pInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="pInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="pInput2" type="data" format="fastqcssanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /> <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"> <option value="ff">FF (for SOLiD)</option> @@ -401,14 +401,14 @@ <test> <!-- Bowtie command: - bowtie -p 4 -S +sam-nohead -q -C chrM_color test-data/bowtie_in1.fastqsanger > test-data/bowtie_out1.sam + bowtie -p 4 -S +sam-nohead -q -C chrM_color test-data/bowtie_in1.fastqcssanger > test-data/bowtie_out1.sam -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes. chrM_color needs to be the base location/name of the index files. --> <param name="genomeSource" value="indexed" /> <param name="index" value="equCab2chrM" /> <param name="sPaired" value="single" /> - <param name="sInput1" ftype="fastqsanger" value="bowtie_in1.fastqsanger" /> + <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" /> <param name="sSettingsType" value="preSet" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out1.sam" /> @@ -417,7 +417,7 @@ <!-- Bowtie command: bowtie-build -f -C test-data/chr_m.fasta chrM_color - bowtie -X 1000 +ff -n 2 -e 70 -l 28 -X 250 +pairtries 100 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color -1 test-data/bowtie_in3.fastqsanger -2 test-data/bowtie_in4.fastqsanger > test-data/bowtie_out3.sam + bowtie -X 1000 +ff -n 2 -e 70 -l 28 -X 250 +pairtries 100 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > test-data/bowtie_out3.sam -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. chrM_base is the index files' location/base name. --> @@ -425,8 +425,8 @@ <param name="ownFile" value="chr_m.fasta" /> <param name="indexSettings" value="indexPreSet" /> <param name="sPaired" value="paired" /> - <param name="pInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" /> - <param name="pInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" /> + <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" /> + <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" /> <param name="pMaxInsert" value="1000" /> <param name="pMateOrient" value="ff" /> <param name="pSettingsType" value="full" /> @@ -460,14 +460,14 @@ <test> <!-- Bowtie command: - bowtie -n 2 -e 70 -l 28 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color test-data/bowtie_in1.fastqsanger > test-data/bowtie_out5.sam + bowtie -n 2 -e 70 -l 28 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color test-data/bowtie_in1.fastqcssanger > test-data/bowtie_out5.sam -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. chrM_base is the index files' location/base name. --> <param name="genomeSource" value="indexed" /> <param name="index" value="equCab2chrM" /> <param name="sPaired" value="single" /> - <param name="sInput1" ftype="fastqsanger" value="bowtie_in1.fastqsanger" /> + <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" /> <param name="sSettingsType" value="full" /> <param name="sSkip" value="0" /> <param name="sAlignLimit" value="-1" /> @@ -496,7 +496,7 @@ <!-- Bowtie command: bowtie-build +noauto +bmaxdivn 4 +dcv 1024 +offrate 5 +ftabchars 10 +little -C -f test-data/chr_m.fasta chrM_color - bowtie -X 1000 +ff -p 4 -S +sam-nohead -q -C chrM_color -1 test-data/bowtie_in3.fastqsanger -2 test-data/bowtie_in4.fastqsanger > test-data/bowtie_out7.sam + bowtie -X 1000 +ff -p 4 -S +sam-nohead -q -C chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > test-data/bowtie_out7.sam -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. chrM_base is the index files' location/base name. --> @@ -517,8 +517,8 @@ <param name="seed" value="-1" /> <param name="cutoff" value="-1" /> <param name="sPaired" value="paired" /> - <param name="pInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" /> - <param name="pInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" /> + <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" /> + <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" /> <param name="pMaxInsert" value="1000" /> <param name="pMateOrient" value="ff" /> <param name="pSettingsType" value="preSet" /> @@ -558,7 +558,7 @@ The output is in SAM format, and has the following columns:: Column Description - -------- -------------------------------------------------------- + -------- -------------------------------------------------------- 1 QNAME Query (pair) NAME 2 FLAG bitwise FLAG 3 RNAME Reference sequence NAME @@ -571,7 +571,7 @@ 10 SEQ query SEQuence on the same strand as the reference 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE - + The flags are as follows:: Flag Description