Mercurial > repos > qfab > bowtie_for_fasta
changeset 4:89563c2b1f71 draft default tip
Uploaded
author | qfab |
---|---|
date | Thu, 28 Aug 2014 20:21:55 -0400 |
parents | d33922d2b6e0 |
children | |
files | bowtie_for_fasta-254d8bd5d21a/bowtie_for_fasta_wrapper.xml |
diffstat | 1 files changed, 46 insertions(+), 102 deletions(-) [+] |
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--- a/bowtie_for_fasta-254d8bd5d21a/bowtie_for_fasta_wrapper.xml Thu Aug 28 20:20:48 2014 -0400 +++ b/bowtie_for_fasta-254d8bd5d21a/bowtie_for_fasta_wrapper.xml Thu Aug 28 20:21:55 2014 -0400 @@ -7,27 +7,20 @@ <command interpreter="python"> bowtie_for_fasta_wrapper.py ## Hackish setting of number of threads - --threads="4" - ## Output - #if str( $outformat) == "sam": - -S "true" - --output "${samoutput}" - #else: - -S "false" - --output "${taboutput}" - #end if - - -## #if $output_unmapped_reads_l -## --output_unmapped_reads="${output_unmapped_reads_l}" -## #end if -## #if $output_suppressed_reads_l -## --output_suppressed_reads="${output_suppressed_reads_l}" -## #end if -## --galaxy_input_format="${singlePaired.sInput1.ext}" + --threads="4" + ## valid Alignments according to the following policy + -n "${validal}" + ## Suppress all alignments for a particular read or pair if more + -m "${suppal}" + ## Report up to int valid alignments + -k "${reportvalal}" + ## The "seed length" + -l "${seedlength}" + ## Mismatched + -e "${maqerr}" + ## The query input files ## Inputs --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper -## --suppressHeader="${suppressHeader}" --genomeSource="${refGenomeSource.genomeSource}" #if $refGenomeSource.genomeSource == "history": ##index already exists @@ -61,31 +54,16 @@ ##use pre-built index --ref="${refGenomeSource.index.fields.path}" #end if - --input1="${sInput1}" - --params="${Params.sSettingsType}" - --mismatchQual="${sMismatchQual}" - --mismatchSeed="${sMismatchSeed}" - --seedLen="${sSeedLen}" - --suppressAlign="${sSuppressAlign}" - --valAlign="${sValAlign}" - #unless $Params.sSettingsType: - --skip="${Params.sSkip}" - --alignLimit="${Params.sAlignLimit}" - --trimH="${Params.sTrimH}" - --trimL="${Params.sTrimL}" - --rounding="${Params.sRounding}" - --maqSoapAlign="${Params.sMaqSoapAlign}" - --tryHard="${Params.sTryHard}" - --best="${Params.sBestOption.sBest}" - #if $Params.sBestOption.sBest == "doBest": - --maxBacktracks="${Params.sBestOption.sdMaxBacktracks}" - --strata="${Params.sBestOption.sdStrata}" - #else: - --maxBacktracks="${Params.sBestOption.snMaxBacktracks}" - #end if - --offrate="${Params.sOffrate}" - --seed="${Params.sSeed}" - #end unless + ##FASTA file + -f "${sInput1}" + ## Output format + #if str( $outformat) == "sam" + -S "true" + -o "${samoutput}" + #else + -S "false" + -o "${fastaoutput}" + #end if </command> <inputs> <conditional name="refGenomeSource"> @@ -151,63 +129,29 @@ </when> <!-- history --> </conditional> <!-- refGenomeSource --> <param name="sInput1" type="data" format="fasta" label="FASTA file" /> - <param name="sMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> - <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> - <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" /> - <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> - <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> - <param name="outformat" size="" type="select" label="Output format"> - <option value="tab">TABULAR</option> - <option value="sam">SAM</option> - </param> - - <conditional name="Params"> - <param name="sSettingsType" type="boolean" checked="true" label="Default settings to use" help="For most mapping needs use Commonly used settings. If you want full control uncheck this box"/> - <when value="true"></when> - <when value="false"> - <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> - <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> - <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> - <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> - <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> - <option value="round">Round to nearest 10</option> - <option value="noRound">Do not round to nearest 10</option> - </param> - <param name="sMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> - <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> - <option value="noTryHard">Do not try hard</option> - <option value="doTryHard">Try hard</option> - </param> - <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> - <option value="noAllValAligns">Do not report all valid alignments</option> - <option value="doAllValAligns">Report all valid alignments</option> - </param> - <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> - <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> - <conditional name="sBestOption"> - <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> - <option value="noBest">Do not use best</option> - <option value="doBest">Use best</option> - </param> - <when value="noBest"> - <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - </when> - <when value="doBest"> - <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - <param name="sdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> - <option value="noStrata">Do not use strata option</option> - <option value="doStrata">Use strata option</option> - </param> - </when> - </conditional> <!-- bestOption --> - <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> - <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> - </when> <!-- full --> - </conditional> + <param name="validal" size="30" type="integer" value="0" label="Number of valid alignments (-n)" > + <validator type="empty_field" message="Enter a valid number of alignements (default 0)"/> + </param> + <param name="suppal" size="30" type="integer" value="1" label="Suppress all alignements if more than" help="Suppress all alignments for a particular read or pair if more than int reportable alignments exist for it" > + <validator type="empty_field" message="Enter a valid number"/> + </param> + <param name="reportvalal" size="30" type="integer" value="1" label="Report up to int valid alignments per read"> + <validator type="empty_field" message="Enter a valid number"/> + </param> + <param name="seedlength" size="30" type="integer" value="36" label="The seed length"> + <validator type="empty_field" message="Enter a valid number"/> + </param> + <param name="maqerr" size="30" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched"> + <validator type="empty_field" message="Enter a valid number"/> + </param> + <param name="outformat" size="" type="select" label="Output format"> + <option value="tab">TABULAR</option> + <option value="sam">SAM</option> + </param> </inputs> - <outputs> + <outputs> <data format="sam" name="samoutput" label="${tool.name} on ${on_string}: SAM"> - <filter>outformat == "sam"</filter> + <filter>outformat == "sam"</filter> <actions> <conditional name="refGenomeSource.genomeSource"> <when value="indexed"> @@ -226,8 +170,8 @@ </conditional> </actions> </data> - <data format="tabular" name="taboutput" label="${tool.name} on ${on_string}: TAB"> - <filter>outformat == "tab"</filter> + <data format="tabular" name="fastaoutput" label="${tool.name} on ${on_string}: TAB"> + <filter>outformat == "tab"</filter> <conditional name="refGenomeSource.genomeSource"> <when value="indexed"> <action type="metadata" name="dbkey"> @@ -243,6 +187,6 @@ </action> </when> </conditional> - </data> + </data> </outputs> </tool>