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author | triasteran |
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date | Wed, 23 Feb 2022 12:17:22 +0000 |
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<tool id="bowtie_remove_rrna_wrapper" name="Remove rRNA using Bowtie" version="0.1.0" python_template_version="2.7"> <requirements> <requirement type="package" version="1.3.1">bowtie</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python2 '__tool_directory__/bowtie_wrapper.py' ## Set number of threads --threads="\${GALAXY_SLOTS:-4}" ## Outputs --output="${output}" #if str( $singlePaired.sPaired ) == "single" #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}" #else #if $output_unmapped_reads_l and $output_unmapped_reads_r --output_unmapped_reads_l="${output_unmapped_reads_l}" --output_unmapped_reads_r="${output_unmapped_reads_r}" #end if #if $output_suppressed_reads_l and $output_suppressed_reads_l --output_suppressed_reads_l="${output_suppressed_reads_l}" --output_suppressed_reads_r="${output_suppressed_reads_r}" #end if --galaxy_input_format="${singlePaired.pInput1.ext}" #end if ## 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 #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): ##user previously built --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" --do_not_build_index #else: ##build index on the fly --ref="${refGenomeSource.ownFile}" --indexSettings="${refGenomeSource.indexParams.indexSettings}" #if $refGenomeSource.indexParams.indexSettings == "indexFull": --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}" #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}" --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}" --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}" --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}" #end if --inodc="${refGenomeSource.indexParams.nodc}" --inoref="${refGenomeSource.indexParams.noref}" --ioffrate="${refGenomeSource.indexParams.offrate}" --iftab="${refGenomeSource.indexParams.ftab}" --intoa="${refGenomeSource.indexParams.ntoa}" --iendian="${refGenomeSource.indexParams.endian}" --iseed="${refGenomeSource.indexParams.seed}" --icutoff="${refGenomeSource.indexParams.cutoff}" #end if #end if #else ##use pre-built index --ref="${refGenomeSource.index.fields.path}" #end if --paired="${singlePaired.sPaired}" #if $singlePaired.sPaired == "single": --input1="${singlePaired.sInput1}" --params="${singlePaired.sParams.sSettingsType}" #if $singlePaired.sParams.sSettingsType == "full": --skip="${singlePaired.sParams.sSkip}" --alignLimit="${singlePaired.sParams.sAlignLimit}" --trimH="${singlePaired.sParams.sTrimH}" --trimL="${singlePaired.sParams.sTrimL}" --mismatchSeed="${singlePaired.sParams.sMismatchSeed}" --mismatchQual="${singlePaired.sParams.sMismatchQual}" --seedLen="${singlePaired.sParams.sSeedLen}" --rounding="${singlePaired.sParams.sRounding}" --maqSoapAlign="${singlePaired.sParams.sMaqSoapAlign}" --reverseAlign="${singlePaired.sParams.sReverseAlign}"<!--Added by Claire for "norc"--> --tryHard="${singlePaired.sParams.sTryHard}" --valAlign="${singlePaired.sParams.sValAlign}" --allValAligns="${singlePaired.sParams.sAllValAligns}" --suppressAlign="${singlePaired.sParams.sSuppressAlign}" --best="${singlePaired.sParams.sBestOption.sBest}" #if $singlePaired.sParams.sBestOption.sBest == "doBest": --maxBacktracks="${singlePaired.sParams.sBestOption.sdMaxBacktracks}" --strata="${singlePaired.sParams.sBestOption.sdStrata}" #else: --maxBacktracks="${singlePaired.sParams.sBestOption.snMaxBacktracks}" #end if --offrate="${singlePaired.sParams.sOffrate}" --seed="${singlePaired.sParams.sSeed}" #end if #else: --input1="${singlePaired.pInput1}" --input2="${singlePaired.pInput2}" --maxInsert="${singlePaired.pMaxInsert}" --mateOrient="${singlePaired.pMateOrient}" --params="${singlePaired.pParams.pSettingsType}" #if $singlePaired.pParams.pSettingsType == "full": --skip="${singlePaired.pParams.pSkip}" --alignLimit="${singlePaired.pParams.pAlignLimit}" --trimH="${singlePaired.pParams.pTrimH}" --trimL="${singlePaired.pParams.pTrimL}" --mismatchSeed="${singlePaired.pParams.pMismatchSeed}" --mismatchQual="${singlePaired.pParams.pMismatchQual}" --seedLen="${singlePaired.pParams.pSeedLen}" --rounding="${singlePaired.pParams.pRounding}" --maqSoapAlign="${singlePaired.pParams.pMaqSoapAlign}" --minInsert="${singlePaired.pParams.pMinInsert}" --maxAlignAttempt="${singlePaired.pParams.pMaxAlignAttempt}" --forwardAlign="${singlePaired.pParams.pForwardAlign}" --reverseAlign="${singlePaired.pParams.pReverseAlign}" --tryHard="${singlePaired.pParams.pTryHard}" --valAlign="${singlePaired.pParams.pValAlign}" --allValAligns="${singlePaired.pParams.pAllValAligns}" --suppressAlign="${singlePaired.pParams.pSuppressAlign}" --best="${singlePaired.pParams.pBestOption.pBest}" #if $singlePaired.pParams.pBestOption.pBest == "doBest": --maxBacktracks="${singlePaired.pParams.pBestOption.pdMaxBacktracks}" --strata="${singlePaired.pParams.pBestOption.pdStrata}" #else: --maxBacktracks="${singlePaired.pParams.pBestOption.pnMaxBacktracks}" #end if --offrate="${singlePaired.pParams.pOffrate}" --seed="${singlePaired.pParams.pSeed}" #end if #end if ]]></command> <inputs> <conditional name="refGenomeSource"> <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param> <when value="indexed"> <param name="index" type="select" label="Select the appropriate rRNA index" help="If the rRNA index for your organism is not listed, you will need to upload a fasta file of the rRNA sequences. "> <options from_data_table="bowtie_rrna_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> </param> </when> <when value="history"> <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" /> <conditional name="indexParams"> <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index"> <option value="indexPreSet">Default</option> <option value="indexFull">Set your own</option> </param> <when value="indexPreSet" /> <when value="indexFull"> <conditional name="autoBehavior"> <param name="autoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv"> <option value="auto">Automatic behavior</option> <option value="set">Set values (sets --noauto and allows others to be set)</option> </param> <when value="auto" /> <when value="set"> <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)"> <option value="unpacked">Use regular representation</option> <option value="packed">Use packed representation</option> </param> <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" /> <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" /> <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> </when> </conditional> <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (with a very repetitive reference)"> <option value="dc">Use difference-cover sample</option> <option value="nodc">Disable difference-cover sample</option> </param> <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)"> <option value="ref">Build all index files</option> <option value="noref">Do not build paired-end alignment index files</option> </param> <param name="offrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" /> <param name="ftab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" /> <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)"> <option value="no">Do not convert Ns</option> <option value="yes">Convert Ns to As</option> </param> <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture"> <option value="little">Little</option> <option value="big">Big</option> </param> <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" /> <param name="cutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" /> </when> <!-- indexFull --> </conditional> <!-- indexParams --> </when> <!-- history --> </conditional> <!-- refGenomeSource --> <conditional name="singlePaired"> <param name="sPaired" type="select" label="Is this library mate-paired?"> <option value="single">Single-end</option> <option value="paired">Paired-end</option> </param> <when value="single"> <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/> <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> <option value="full" selected="true">Full parameter list</option> </param> <when value="preSet" /> <when value="full"> <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="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="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> <param name="sSeedLen" type="integer" value="25" label="Seed length (-l)" help="Minimum value is 5" /> <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="3" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> <param name="sReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> <!--Added by Claire--> <option value="noReverse">Do not align against the reverse-complement reference strand</option> <option value="reverse">Align against the reverse-complement reference strand</option> </param> <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="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" /> <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="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="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="True" 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> <!-- sParams --> </when> <!-- single --> <when value="paired"> <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> </options> </param> <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="fr">FR (for Illumina)</option> <option value="rf">RF</option> <option value="ff">FF (for SOLiD)</option> </param> <conditional name="pParams"> <param name="pSettingsType" 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> <option value="full">Full parameter list</option> </param> <when value="preSet" /> <when value="full"> <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> <param name="pMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> <param name="pSeedLen" type="integer" value="25" label="Seed length (-l)" help="Minimum value is 5" /> <param name="pRounding" 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="pMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> <param name="pMaxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" /> <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)"> <option value="forward">Align against the forward reference strand</option> <option value="noForward">Do not align against the forward reference strand</option> </param> <param name="pReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> <option value="reverse">Align against the reverse-complement reference strand</option> <option value="noReverse">Do not align against the reverse-complement reference strand</option> </param> <param name="pTryHard" 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="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" /> <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> <option value="noAllValAligns">Do not report all valid alignments</option> <option value="doAllValAligns">Report all valid alignments</option> </param> <param name="pSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" /> <param name="pMaxFile" 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="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> <conditional name="pBestOption"> <param name="pBest" 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="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> </when> <when value="doBest"> <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> <param name="pdStrata" 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> <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> </when> <!-- full --> </conditional> <!-- pParams --> </when> <!-- paired --> </conditional> <!-- singlePaired --> <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" /> </inputs> <outputs> <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> <actions> <conditional name="refGenomeSource.genomeSource"> <when value="indexed"> <action type="metadata" name="dbkey"> <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="refGenomeSource.index" column="0"/> </option> </action> </when> <when value="history"> <action type="metadata" name="dbkey"> <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> <filter>(( singlePaired['sPaired'] == "single" and singlePaired['sParams']['sSettingsType'] == "full" and singlePaired['sParams']['sMaxFile'] is True ) or ( singlePaired['sPaired'] == "paired" and singlePaired['pParams']['pSettingsType'] == "full" and singlePaired['pParams']['pMaxFile'] is True )) </filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"> <filter>singlePaired['sPaired'] == "paired"</filter> <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> <filter>singlePaired['pParams']['pMaxFile'] is True</filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"> <filter> (( singlePaired['sPaired'] == "single" and singlePaired['sParams']['sSettingsType'] == "full" and singlePaired['sParams']['sUnmappedFile'] is True ) or ( singlePaired['sPaired'] == "paired" and singlePaired['pParams']['pSettingsType'] == "full" and singlePaired['pParams']['pUnmappedFile'] is True )) </filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> <filter>singlePaired['sPaired'] == "paired"</filter> <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> </outputs> <tests> <test> <!-- Bowtie command: bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam sort bowtie_out6_u.sam > bowtie_out6.sam -p is the number of threads. You need to replace the + with 2 dashes. chrM_base needs to be the base location/name of the index files. --> <param name="genomeSource" value="indexed" /> <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> <param name="index" value="equCab2chrM" /> <param name="sPaired" value="single" /> <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> <param name="sSettingsType" value="preSet" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" /> </test> <test> <!-- Bowtie command: bowtie-build -f test-data/phiX.fasta phiX_base bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam sort bowtie_out7_u.sam > bowtie_out7.sam sort bowtie_out8_u_1.sam > bowtie_out8_1.sam sort bowtie_out8_u_2.sam > bowtie_out8_2.sam Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines. -p is the number of threads. You need to replace the + with 2 dashes. The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq. chrM_base is the index files' location/base name. --> <param name="genomeSource" value="history" /> <param name="ownFile" value="phiX.fasta" /> <param name="indexSettings" value="indexPreSet" /> <param name="sPaired" value="paired" /> <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> <param name="pMaxInsert" value="1000" /> <param name="pMateOrient" value="ff" /> <param name="pSettingsType" value="full" /> <param name="pSkip" value="0" /> <param name="pAlignLimit" value="-1" /> <param name="pTrimH" value="0" /> <param name="pTrimL" value="0" /> <param name="pMismatchSeed" value="2" /> <param name="pMismatchQual" value="70" /> <param name="pSeedLen" value="25" /> <param name="pRounding" value="round" /> <param name="pMaqSoapAlign" value="-1" /> <param name="pMinInsert" value="0" /> <param name="pMaxAlignAttempt" value="100" /> <param name="pForwardAlign" value="forward" /> <param name="pReverseAlign" value="reverse" /> <param name="pTryHard" value="noTryHard" /> <param name="pValAlign" value="1" /> <param name="pAllValAligns" value="noAllValAligns" /> <param name="pSuppressAlign" value="-1" /> <param name="pUnmappedFile" value="true" /> <param name="pMaxFile" value="false" /> <param name="pBest" value="doBest" /> <param name="pdMaxBacktracks" value="800" /> <param name="pdStrata" value="noStrata" /> <param name="pOffrate" value="-1" /> <param name="pSeed" value="-1" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" /> <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" /> </test> <!-- start testing of non-sanger variant fastq reads --> <test> <param name="genomeSource" value="history" /> <param name="ownFile" value="phiX.fasta" /> <param name="indexSettings" value="indexPreSet" /> <param name="sPaired" value="paired" /> <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" /> <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" /> <param name="pMaxInsert" value="1000" /> <param name="pMateOrient" value="ff" /> <param name="pSettingsType" value="full" /> <param name="pSkip" value="0" /> <param name="pAlignLimit" value="-1" /> <param name="pTrimH" value="0" /> <param name="pTrimL" value="0" /> <param name="pMismatchSeed" value="2" /> <param name="pMismatchQual" value="70" /> <param name="pSeedLen" value="25" /> <param name="pRounding" value="round" /> <param name="pMaqSoapAlign" value="-1" /> <param name="pMinInsert" value="0" /> <param name="pMaxAlignAttempt" value="100" /> <param name="pForwardAlign" value="forward" /> <param name="pReverseAlign" value="reverse" /> <param name="pTryHard" value="noTryHard" /> <param name="pValAlign" value="1" /> <param name="pAllValAligns" value="noAllValAligns" /> <param name="pSuppressAlign" value="-1" /> <param name="pUnmappedFile" value="true" /> <param name="pMaxFile" value="false" /> <param name="pBest" value="doBest" /> <param name="pdMaxBacktracks" value="800" /> <param name="pdStrata" value="noStrata" /> <param name="pOffrate" value="-1" /> <param name="pSeed" value="-1" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> <output name="output_unmapped_reads_l" ftype="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" sort="True" /> <output name="output_unmapped_reads_r" ftype="fastqillumna" file="bowtie_out8_2.fastqillumina.sorted" sort="True" /> </test> <test> <param name="genomeSource" value="history" /> <param name="ownFile" value="phiX.fasta" /> <param name="indexSettings" value="indexPreSet" /> <param name="sPaired" value="paired" /> <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" /> <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" /> <param name="pMaxInsert" value="1000" /> <param name="pMateOrient" value="ff" /> <param name="pSettingsType" value="full" /> <param name="pSkip" value="0" /> <param name="pAlignLimit" value="-1" /> <param name="pTrimH" value="0" /> <param name="pTrimL" value="0" /> <param name="pMismatchSeed" value="2" /> <param name="pMismatchQual" value="70" /> <param name="pSeedLen" value="25" /> <param name="pRounding" value="round" /> <param name="pMaqSoapAlign" value="-1" /> <param name="pMinInsert" value="0" /> <param name="pMaxAlignAttempt" value="100" /> <param name="pForwardAlign" value="forward" /> <param name="pReverseAlign" value="reverse" /> <param name="pTryHard" value="noTryHard" /> <param name="pValAlign" value="1" /> <param name="pAllValAligns" value="noAllValAligns" /> <param name="pSuppressAlign" value="-1" /> <param name="pUnmappedFile" value="true" /> <param name="pMaxFile" value="false" /> <param name="pBest" value="doBest" /> <param name="pdMaxBacktracks" value="800" /> <param name="pdStrata" value="noStrata" /> <param name="pOffrate" value="-1" /> <param name="pSeed" value="-1" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" /> <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" /> </test> <!-- end testing of non-sanger variant fastq reads --> <test> <!-- Bowtie command: bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 25 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam sort bowtie_out9_u.sam > bowtie_out9.sam -p is the number of threads. You need to replace the + with 2 dashes. chrM_base is the index files' location/base name. --> <param name="genomeSource" value="indexed" /> <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> <param name="index" value="equCab2chrM" /> <param name="sPaired" value="single" /> <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> <param name="sSettingsType" value="full" /> <param name="sSkip" value="0" /> <param name="sAlignLimit" value="-1" /> <param name="sTrimH" value="0" /> <param name="sTrimL" value="0" /> <param name="sMismatchSeed" value="2" /> <param name="sMismatchQual" value="70" /> <param name="sSeedLen" value="25" /> <param name="sRounding" value="round" /> <param name="sMaqSoapAlign" value="-1" /> <param name="sTryHard" value="doTryHard" /> <param name="sValAlign" value="1" /> <param name="sAllValAligns" value="noAllValAligns" /> <param name="sSuppressAlign" value="-1" /> <param name="sUnmappedFile" value="false" /> <param name="sMaxFile" value="false" /> <param name="sBest" value="noBest" /> <param name="snMaxBacktracks" value="125" /> <param name="sOffrate" value="-1" /> <param name="sSeed" value="-1" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" /> </test> <test> <!-- Bowtie command: bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam sort bowtie_out10_u.sam > bowtie_out10.sam -p is the number of threads. You need to replace the + with 2 dashes. chrM_base is the index files' location/base name. --> <param name="genomeSource" value="history" /> <param name="ownFile" value="phiX.fasta" /> <param name="indexSettings" value="indexFull" /> <param name="autoB" value="auto" /> <param name="nodc" value="dc" /> <param name="noref" value="ref" /> <param name="offrate" value="5" /> <param name="ftab" value="10" /> <param name="ntoa" value="no" /> <param name="endian" value="little" /> <param name="seed" value="-1" /> <param name="cutoff" value="-1" /> <param name="sPaired" value="paired" /> <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> <param name="pMaxInsert" value="1000" /> <param name="pMateOrient" value="ff" /> <param name="pSettingsType" value="preSet" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" /> </test> </tests> <help> <![CDATA[ Bowtie is a short read aligner. ]]> </help> <citations> <citation type="bibtex"> @misc{githubbowtie, author = {LastTODO, FirstTODO}, year = {TODO}, title = {bowtie}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/BenLangmead/bowtie}, }</citation> </citations> </tool>