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Updated Bowtie wrapper for new fastqcssanger datatype, and added equCab2 to builds.txt so sam_to_bam and sam_pileup will pass

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Kelly Vincent
2010-03-03 15:37:43 -05:00
parent 1b973215f3
commit 7403f4301b
2 changed files with 17 additions and 16 deletions
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tool-data/shared/ucsc/builds.txt
+1
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@@ -786,6 +786,7 @@ eschColi_K12 Escherichia coli K12 (eschColi_K12)
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
tools/sr_mapping/bowtie_color_wrapper.xml
+16 -16
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@@ -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 @@ Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare yo
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 @@ The output is in SAM format, and has the following columns::
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