Mercurial > repos > triasteran > bowtie_remove_rrna_wrapper

--- a/bowtie_remove_rrna_wrapper/.hgignore	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-syntax: glob
-.idea
--- a/bowtie_remove_rrna_wrapper/bowtie_indices.loc.sample	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Mouse_rRNA	Mouse_rRNA	Mouse_rRNA	/home/DATA/galaxy/galaxy-dist/data/indexes/bowtie_rrna_indexes/Mouse_rRNA/bowtie_rrna_indexes/mouse_rRNA_index
--- a/bowtie_remove_rrna_wrapper/bowtie_remove_rrna_wrapper.xml	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,681 +0,0 @@
-<tool id="bowtie_remove_rrna_wrapper" name="Remove rRNA using Bowtie" version="0.1.1a">
-    <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="${singlePaired.sParams.sReverseAlign}"
-          --tryHard="${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)">
-              <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>
--- a/bowtie_remove_rrna_wrapper/bowtie_wrapper.py	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,469 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Runs Bowtie on single-end or paired-end data.
-For use with Bowtie v. 0.12.7
-
-usage: bowtie_wrapper.py [options]
-    -t, --threads=t: The number of threads to run
-    -o, --output=o: The output file
-    --output_unmapped_reads=: File name for unmapped reads (single-end)
-    --output_unmapped_reads_l=: File name for unmapped reads (left, paired-end)
-    --output_unmapped_reads_r=: File name for unmapped reads (right, paired-end)
-    --output_suppressed_reads=: File name for suppressed reads because of max setting (single-end)
-    --output_suppressed_reads_l=: File name for suppressed reads because of max setting (left, paired-end)
-    --output_suppressed_reads_r=: File name for suppressed reads because of max setting (right, paired-end)
-    -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format
-    -I, --input2=I: The reverse reads file in Sanger FASTQ format
-    -4, --dataType=4: The type of data (SOLiD or Solexa)
-    -2, --paired=2: Whether the data is single- or paired-end
-    -g, --genomeSource=g: The type of reference provided
-    -r, --ref=r: The reference genome to use or index
-    -s, --skip=s: Skip the first n reads
-    -a, --alignLimit=a: Only align the first n reads
-    -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment
-    -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment
-    -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed
-    -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions
-    -l, --seedLen=l: Seed length
-    -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30
-    -P, --maqSoapAlign=P: Choose MAQ- or SOAP-like alignment policy
-    -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist
-    -v, --valAlign=v: Report up to n valid arguments per read
-    -V, --allValAligns=V: Whether or not to report all valid alignments per read
-    -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist
-    -b, --best=b: 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
-    -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read
-    -R, --strata=R: Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable
-    -j, --minInsert=j: Minimum insert size for valid paired-end alignments
-    -J, --maxInsert=J: Maximum insert size for valid paired-end alignments
-    -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand
-    -A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate
-    -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand
-    -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand
-    -F, --offrate=F: Override the offrate of the index to n
-    -8, --snpphred=8: SNP penalty on Phred scale
-    -6, --snpfrac=6: Fraction of sites expected to be SNP sites
-    -7, --keepends=7: Keep extreme-end nucleotides and qualities
-    -S, --seed=S: Seed for pseudo-random number generator
-    -C, --params=C: Whether to use default or specified parameters
-    -u, --iautoB=u: Automatic or specified behavior
-    -K, --ipacked=K: Whether or not to use a packed representation for DNA strings
-    -Q, --ibmax=Q: Maximum number of suffixes allowed in a block
-    -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference
-    -D, --idcv=D: The period for the difference-cover sample
-    -U, --inodc=U: Whether or not to disable the use of the difference-cover sample
-    -y, --inoref=y: Whether or not to build the part of the reference index used only in paired-end alignment
-    -z, --ioffrate=z: How many rows get marked during annotation of some or all of the Burrows-Wheeler rows
-    -W, --iftab=W: The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query
-    -X, --intoa=X: Whether or not to convert Ns in the reference sequence to As
-    -N, --iendian=N: Endianness to use when serializing integers to the index file
-    -Z, --iseed=Z: Seed for the pseudorandom number generator
-    -c, --icutoff=c: Number of first bases of the reference sequence to index
-    -x, --indexSettings=x: Whether or not indexing options are to be set
-    -H, --suppressHeader=H: Suppress header
-    --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
-"""
-
-import optparse, os, shutil, subprocess, sys, tempfile
-
-#Allow more than Sanger encoded variants
-DEFAULT_ASCII_ENCODING = '--phred33-quals'
-GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = { 'fastqsanger':'--phred33-quals', 'fastqillumina':'--phred64-quals', 'fastqsolexa':'--solexa-quals' }
-#FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config
-
-def stop_err( msg ):
-    sys.stderr.write( '%s\n' % msg )
-    sys.exit()
-
-def __main__():
-    #Parse Command Line
-    parser = optparse.OptionParser()
-    parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' )
-    parser.add_option( '-o', '--output', dest='output', help='The output file' )
-    parser.add_option( '', '--output_unmapped_reads', dest='output_unmapped_reads', help='File name for unmapped reads (single-end)' )
-    parser.add_option( '', '--output_unmapped_reads_l', dest='output_unmapped_reads_l', help='File name for unmapped reads (left, paired-end)' )
-    parser.add_option( '', '--output_unmapped_reads_r', dest='output_unmapped_reads_r', help='File name for unmapped reads (right, paired-end)' )
-    parser.add_option( '', '--output_suppressed_reads', dest='output_suppressed_reads', help='File name for suppressed reads because of max setting (single-end)' )
-    parser.add_option( '', '--output_suppressed_reads_l', dest='output_suppressed_reads_l', help='File name for suppressed reads because of max setting (left, paired-end)' )
-    parser.add_option( '', '--output_suppressed_reads_r', dest='output_suppressed_reads_r', help='File name for suppressed reads because of max setting (right, paired-end)' )
-    parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' )
-    parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
-    parser.add_option( '-I', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
-    parser.add_option( '-2', '--paired', dest='paired', help='Whether the data is single- or paired-end' )
-    parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' )
-    parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
-    parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' )
-    parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' )
-    parser.add_option( '-T', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment' )
-    parser.add_option( '-L', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment' )
-    parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' )
-    parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' )
-    parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' )
-    parser.add_option( '-n', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30' )
-    parser.add_option( '-P', '--maqSoapAlign', dest='maqSoapAlign', help='Choose MAQ- or SOAP-like alignment policy' )
-    parser.add_option( '-w', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist' )
-    parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid arguments per read' )
-    parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read' )
-    parser.add_option( '-G', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist' )
-    parser.add_option( '-b', '--best', dest='best', help="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" )
-    parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' )
-    parser.add_option( '-R', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable' )
-    parser.add_option( '-j', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments' )
-    parser.add_option( '-J', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments' )
-    parser.add_option( '-O', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand' )
-    parser.add_option( '-A', '--maxAlignAttempt', dest='maxAlignAttempt', help='Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate' )
-    parser.add_option( '-f', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand' )
-    parser.add_option( '-E', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand' )
-    parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' )
-    parser.add_option( '-S', '--seed', dest='seed', help='Seed for pseudo-random number generator' )
-    parser.add_option( '-8', '--snpphred', dest='snpphred', help='SNP penalty on Phred scale' )
-    parser.add_option( '-6', '--snpfrac', dest='snpfrac', help='Fraction of sites expected to be SNP sites' )
-    parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' )
-    parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' )
-    parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' )
-    parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' )
-    parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' )
-    parser.add_option( '-Y', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference' )
-    parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' )
-    parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' )
-    parser.add_option( '-y', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paired-end alignment' )
-    parser.add_option( '-z', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows' )
-    parser.add_option( '-W', '--iftab', dest='iftab', help='The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query' )
-    parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' )
-    parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' )
-    parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' )
-    parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index' )
-    parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' )
-    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
-    parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' )
-    parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' )
-    (options, args) = parser.parse_args()
-    stdout = ''
-
-    # make temp directory for placement of indices and copy reference file there if necessary
-    tmp_index_dir = tempfile.mkdtemp()
-    # get type of data (solid or solexa)
-    if options.dataType == 'solid':
-        colorspace = '-C'
-    else:
-        colorspace = ''
-    # index if necessary
-    if options.genomeSource == 'history' and not options.do_not_build_index:
-        # set up commands
-        if options.index_settings =='indexPreSet':
-            indexing_cmds = '%s' % colorspace
-        else:
-            try:
-                if options.iautoB and options.iautoB == 'set':
-                    iautoB = '--noauto'
-                else:
-                    iautoB = ''
-                if options. ipacked and options.ipacked == 'packed':
-                    ipacked = '--packed'
-                else:
-                    ipacked = ''
-                if options.ibmax and int( options.ibmax ) >= 1:
-                    ibmax = '--bmax %s' % options.ibmax
-                else:
-                    ibmax = ''
-                if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0:
-                    ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn
-                else:
-                    ibmaxdivn = ''
-                if options.idcv and int( options.idcv ) > 0:
-                    idcv = '--dcv %s' % options.idcv
-                else:
-                    idcv = ''
-                if options.inodc and options.inodc == 'nodc':
-                    inodc = '--nodc'
-                else:
-                    inodc = ''
-                if options.inoref and options.inoref == 'noref':
-                    inoref = '--noref'
-                else:
-                    inoref = ''
-                if options.iftab and int( options.iftab ) >= 0:
-                    iftab = '--ftabchars %s' % options.iftab
-                else:
-                    iftab = ''
-                if options.intoa and options.intoa == 'yes':
-                    intoa = '--ntoa'
-                else:
-                    intoa = ''
-                if options.iendian and options.iendian == 'big':
-                    iendian = '--big'
-                else:
-                    iendian = '--little'
-                if options.iseed and int( options.iseed ) > 0:
-                    iseed = '--seed %s' % options.iseed
-                else:
-                    iseed = ''
-                if options.icutoff and int( options.icutoff ) > 0:
-                    icutoff = '--cutoff %s' % options.icutoff
-                else:
-                    icutoff = ''
-                indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \
-                                ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,
-                                  inoref, options.ioffrate, iftab, intoa, iendian,
-                                  iseed, icutoff, colorspace )
-            except ValueError, e:
-                # clean up temp dir
-                if os.path.exists( tmp_index_dir ):
-                    shutil.rmtree( tmp_index_dir )
-                stop_err( "Something is wrong with the indexing parameters and the indexing and alignment could not be run. Make sure you don't have any non-numeric values where they should be numeric.\n" + str( e ) )
-        ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
-        ref_file_name = ref_file.name
-        ref_file.close()
-        os.symlink( options.ref, ref_file_name )
-        cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name )
-        try:
-            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
-            tmp_stderr = open( tmp, 'wb' )
-            proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
-            returncode = proc.wait()
-            tmp_stderr.close()
-            # get stderr, allowing for case where it's very large
-            tmp_stderr = open( tmp, 'rb' )
-            stderr = ''
-            buffsize = 1048576
-            try:
-                while True:
-                    stderr += tmp_stderr.read( buffsize )
-                    if not stderr or len( stderr ) % buffsize != 0:
-                        break
-            except OverflowError:
-                pass
-            tmp_stderr.close()
-            if returncode != 0:
-                raise (Exception, stderr)
-        except Exception, e:
-            # clean up temp dir
-            if os.path.exists( tmp_index_dir ):
-                shutil.rmtree( tmp_index_dir )
-            stop_err( 'Error indexing reference sequence\n' + str( e ) )
-        stdout += 'File indexed. '
-    else:
-        ref_file_name = options.ref
-    # set up aligning and generate aligning command options
-    # automatically set threads in both cases
-    tmp_suppressed_file_name = None
-    tmp_unmapped_file_name = None
-    if options.suppressHeader == 'true':
-        suppressHeader = '--sam-nohead'
-    else:
-        suppressHeader = ''
-    if options.maxInsert and int( options.maxInsert ) > 0:
-        maxInsert = '-X %s' % options.maxInsert
-    else:
-        maxInsert = ''
-    if options.mateOrient:
-        mateOrient = '--%s' % options.mateOrient
-    else:
-        mateOrient = ''
-    quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING )
-    if options.params == 'preSet':
-        aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \
-                ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding )
-    else:
-        try:
-            if options.skip and int( options.skip ) > 0:
-                skip = '-s %s' % options.skip
-            else:
-                skip = ''
-            if options.alignLimit and int( options.alignLimit ) >= 0:
-                alignLimit = '-u %s' % options.alignLimit
-            else:
-                alignLimit = ''
-            if options.trimH and int( options.trimH ) > 0:
-                trimH = '-5 %s' % options.trimH
-            else:
-                trimH = ''
-            if options.trimL and int( options.trimL ) > 0:
-                trimL = '-3 %s' % options.trimL
-            else:
-                trimL = ''
-            if options.maqSoapAlign != '-1' and int( options.maqSoapAlign ) >= 0:
-                maqSoapAlign = '-v %s' % options.maqSoapAlign
-            else:
-                maqSoapAlign = ''
-            if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \
-                        or options.mismatchSeed == '2' or options.mismatchSeed == '3'):
-                mismatchSeed = '-n %s' % options.mismatchSeed
-            else:
-                mismatchSeed = ''
-            if options.mismatchQual and int( options.mismatchQual ) >= 0:
-                mismatchQual = '-e %s' % options.mismatchQual
-            else:
-                mismatchQual = ''
-            if options.seedLen and int( options.seedLen ) >= 5:
-                seedLen = '-l %s' % options.seedLen
-            else:
-                seedLen = ''
-            if options.rounding == 'noRound':
-                rounding = '--nomaqround'
-            else:
-                rounding = ''
-            if options.minInsert and int( options.minInsert ) > 0:
-                minInsert = '-I %s' % options.minInsert
-            else:
-                minInsert = ''
-            if options.maxAlignAttempt and int( options.maxAlignAttempt ) >= 0:
-                maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt
-            else:
-                maxAlignAttempt = ''
-            if options.forwardAlign == 'noForward':
-                forwardAlign = '--nofw'
-            else:
-                forwardAlign = ''
-            if options.reverseAlign == 'noReverse':
-                reverseAlign = '--norc'
-            else:
-                reverseAlign = ''
-            if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \
-                    ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ):
-                maxBacktracks = '--maxbts %s' % options.maxBacktracks
-            else:
-                maxBacktracks = ''
-            if options.tryHard == 'doTryHard':
-                tryHard = '-y'
-            else:
-                tryHard = ''
-            if options.valAlign and int( options.valAlign ) >= 0:
-                valAlign = '-k %s' % options.valAlign
-            else:
-                valAlign = ''
-            if options.allValAligns == 'doAllValAligns':
-                allValAligns = '-a'
-            else:
-                allValAligns = ''
-            if options.suppressAlign and int( options.suppressAlign ) >= 0:
-                suppressAlign = '-m %s' % options.suppressAlign
-            else:
-                suppressAlign = ''
-            if options.best == 'doBest':
-                best = '--best'
-            else:
-                best = ''
-            if options.strata == 'doStrata':
-                strata = '--strata'
-            else:
-                strata = ''
-            if options.offrate and int( options.offrate ) >= 0:
-                offrate = '-o %s' % options.offrate
-            else:
-                offrate = ''
-            if options.seed and int( options.seed ) >= 0:
-                seed = '--seed %s' % options.seed
-            else:
-                seed = ''
-            if options.paired == 'paired':
-                if options.output_unmapped_reads_l and options.output_unmapped_reads_r:
-                    tmp_unmapped_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
-                    tmp_unmapped_file_name = tmp_unmapped_file.name
-                    tmp_unmapped_file.close()
-                    output_unmapped_reads = '--un %s' % tmp_unmapped_file_name
-                else:
-                    output_unmapped_reads = ''
-                if options.output_suppressed_reads:
-                    tmp_suppressed_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
-                    tmp_suppressed_file_name = tmp_suppressed_file.name
-                    tmp_suppressed_file.close()
-                    output_suppressed_reads = '--max %s' % tmp_suppressed_file_name
-                else:
-                    output_suppressed_reads = ''
-            else:
-                if options.output_unmapped_reads:
-                    output_unmapped_reads = '--un %s' % options.output_unmapped_reads
-                else:
-                    output_unmapped_reads = ''
-                if options.output_suppressed_reads:
-                    output_suppressed_reads = '--max %s' % options.output_suppressed_reads
-                else:
-                    output_suppressed_reads = ''
-            snpfrac = ''
-            if options.snpphred and int( options.snpphred ) >= 0:
-                snpphred = '--snpphred %s' % options.snpphred
-            else:
-                snpphred = ''
-                if options.snpfrac and float( options.snpfrac ) >= 0:
-                    snpfrac = '--snpfrac %s' % options.snpfrac
-            if options.keepends and options.keepends == 'doKeepends':
-                keepends = '--col-keepends'
-            else:
-                keepends = ''
-            aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \
-                            '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
-                            ( maxInsert, mateOrient, options.threads, suppressHeader,
-                              colorspace, skip, alignLimit, trimH, trimL, maqSoapAlign,
-                              mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
-                              maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,
-                              tryHard, valAlign, allValAligns, suppressAlign, best,
-                              strata, offrate, seed, snpphred, snpfrac, keepends,
-                              output_unmapped_reads, output_suppressed_reads,
-                              quality_score_encoding )
-        except ValueError, e:
-            # clean up temp dir
-            if os.path.exists( tmp_index_dir ):
-                shutil.rmtree( tmp_index_dir )
-            stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
-    try:
-        # have to nest try-except in try-finally to handle 2.4
-        try:
-            # prepare actual mapping commands
-            if options.paired == 'paired':
-                cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
-            else:
-                cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
-            # align
-            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
-            tmp_stderr = open( tmp, 'wb' )
-            proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
-            returncode = proc.wait()
-            tmp_stderr.close()
-            # get stderr, allowing for case where it's very large
-            tmp_stderr = open( tmp, 'rb' )
-            stderr = ''
-            buffsize = 1048576
-            try:
-                while True:
-                    stderr += tmp_stderr.read( buffsize )
-                    if not stderr or len( stderr ) % buffsize != 0:
-                        break
-            except OverflowError:
-                pass
-            tmp_stderr.close()
-            if returncode != 0:
-                raise (Exception, stderr)
-            # get suppressed and unmapped reads output files in place if appropriate
-            if options.paired == 'paired' and tmp_suppressed_file_name and \
-                               options.output_suppressed_reads_l and options.output_suppressed_reads_r:
-                try:
-                    left = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
-                    right = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
-                    shutil.move( left, options.output_suppressed_reads_l )
-                    shutil.move( right, options.output_suppressed_reads_r )
-                except Exception, e:
-                    sys.stdout.write( 'Error producing the suppressed output file.\n' )
-            if options.paired == 'paired' and tmp_unmapped_file_name and \
-                               options.output_unmapped_reads_l and options.output_unmapped_reads_r:
-                try:
-                    left = tmp_unmapped_file_name.replace( '.fastq', '_1.fastq' )
-                    right = tmp_unmapped_file_name.replace( '.fastq', '_2.fastq' )
-                    shutil.move( left, options.output_unmapped_reads_l )
-                    shutil.move( right, options.output_unmapped_reads_r )
-                except Exception, e:
-                    sys.stdout.write( 'Error producing the unmapped output file.\n' )
-            # check that there are results in the output file
-            if os.path.getsize( options.output ) == 0:
-                raise (Exception, 'The output file is empty, there may be an error with your input file or settings.')
-        except Exception, e:
-            stop_err( 'Error aligning sequence. ' + str( e ) )
-    finally:
-        # clean up temp dir
-        if os.path.exists( tmp_index_dir ):
-            shutil.rmtree( tmp_index_dir )
-    stdout += 'Sequence file aligned.\n'
-    sys.stdout.write( stdout )
-
-if __name__=="__main__": __main__()
--- a/bowtie_remove_rrna_wrapper/bowtie_wrapper_py3.py	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,469 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Runs Bowtie on single-end or paired-end data.
-For use with Bowtie v. 0.12.7
-
-usage: bowtie_wrapper.py [options]
-    -t, --threads=t: The number of threads to run
-    -o, --output=o: The output file
-    --output_unmapped_reads=: File name for unmapped reads (single-end)
-    --output_unmapped_reads_l=: File name for unmapped reads (left, paired-end)
-    --output_unmapped_reads_r=: File name for unmapped reads (right, paired-end)
-    --output_suppressed_reads=: File name for suppressed reads because of max setting (single-end)
-    --output_suppressed_reads_l=: File name for suppressed reads because of max setting (left, paired-end)
-    --output_suppressed_reads_r=: File name for suppressed reads because of max setting (right, paired-end)
-    -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format
-    -I, --input2=I: The reverse reads file in Sanger FASTQ format
-    -4, --dataType=4: The type of data (SOLiD or Solexa)
-    -2, --paired=2: Whether the data is single- or paired-end
-    -g, --genomeSource=g: The type of reference provided
-    -r, --ref=r: The reference genome to use or index
-    -s, --skip=s: Skip the first n reads
-    -a, --alignLimit=a: Only align the first n reads
-    -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment
-    -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment
-    -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed
-    -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions
-    -l, --seedLen=l: Seed length
-    -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30
-    -P, --maqSoapAlign=P: Choose MAQ- or SOAP-like alignment policy
-    -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist
-    -v, --valAlign=v: Report up to n valid arguments per read
-    -V, --allValAligns=V: Whether or not to report all valid alignments per read
-    -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist
-    -b, --best=b: 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
-    -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read
-    -R, --strata=R: Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable
-    -j, --minInsert=j: Minimum insert size for valid paired-end alignments
-    -J, --maxInsert=J: Maximum insert size for valid paired-end alignments
-    -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand
-    -A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate
-    -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand
-    -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand
-    -F, --offrate=F: Override the offrate of the index to n
-    -8, --snpphred=8: SNP penalty on Phred scale
-    -6, --snpfrac=6: Fraction of sites expected to be SNP sites
-    -7, --keepends=7: Keep extreme-end nucleotides and qualities
-    -S, --seed=S: Seed for pseudo-random number generator
-    -C, --params=C: Whether to use default or specified parameters
-    -u, --iautoB=u: Automatic or specified behavior
-    -K, --ipacked=K: Whether or not to use a packed representation for DNA strings
-    -Q, --ibmax=Q: Maximum number of suffixes allowed in a block
-    -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference
-    -D, --idcv=D: The period for the difference-cover sample
-    -U, --inodc=U: Whether or not to disable the use of the difference-cover sample
-    -y, --inoref=y: Whether or not to build the part of the reference index used only in paired-end alignment
-    -z, --ioffrate=z: How many rows get marked during annotation of some or all of the Burrows-Wheeler rows
-    -W, --iftab=W: The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query
-    -X, --intoa=X: Whether or not to convert Ns in the reference sequence to As
-    -N, --iendian=N: Endianness to use when serializing integers to the index file
-    -Z, --iseed=Z: Seed for the pseudorandom number generator
-    -c, --icutoff=c: Number of first bases of the reference sequence to index
-    -x, --indexSettings=x: Whether or not indexing options are to be set
-    -H, --suppressHeader=H: Suppress header
-    --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
-"""
-
-import optparse, os, shutil, subprocess, sys, tempfile
-
-#Allow more than Sanger encoded variants
-DEFAULT_ASCII_ENCODING = '--phred33-quals'
-GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = { 'fastqsanger':'--phred33-quals', 'fastqillumina':'--phred64-quals', 'fastqsolexa':'--solexa-quals' }
-#FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config
-
-def stop_err( msg ):
-    sys.stderr.write( '%s\n' % msg )
-    sys.exit()
-
-def __main__():
-    #Parse Command Line
-    parser = optparse.OptionParser()
-    parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' )
-    parser.add_option( '-o', '--output', dest='output', help='The output file' )
-    parser.add_option( '', '--output_unmapped_reads', dest='output_unmapped_reads', help='File name for unmapped reads (single-end)' )
-    parser.add_option( '', '--output_unmapped_reads_l', dest='output_unmapped_reads_l', help='File name for unmapped reads (left, paired-end)' )
-    parser.add_option( '', '--output_unmapped_reads_r', dest='output_unmapped_reads_r', help='File name for unmapped reads (right, paired-end)' )
-    parser.add_option( '', '--output_suppressed_reads', dest='output_suppressed_reads', help='File name for suppressed reads because of max setting (single-end)' )
-    parser.add_option( '', '--output_suppressed_reads_l', dest='output_suppressed_reads_l', help='File name for suppressed reads because of max setting (left, paired-end)' )
-    parser.add_option( '', '--output_suppressed_reads_r', dest='output_suppressed_reads_r', help='File name for suppressed reads because of max setting (right, paired-end)' )
-    parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' )
-    parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
-    parser.add_option( '-I', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
-    parser.add_option( '-2', '--paired', dest='paired', help='Whether the data is single- or paired-end' )
-    parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' )
-    parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
-    parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' )
-    parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' )
-    parser.add_option( '-T', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment' )
-    parser.add_option( '-L', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment' )
-    parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' )
-    parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' )
-    parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' )
-    parser.add_option( '-n', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30' )
-    parser.add_option( '-P', '--maqSoapAlign', dest='maqSoapAlign', help='Choose MAQ- or SOAP-like alignment policy' )
-    parser.add_option( '-w', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist' )
-    parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid arguments per read' )
-    parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read' )
-    parser.add_option( '-G', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist' )
-    parser.add_option( '-b', '--best', dest='best', help="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" )
-    parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' )
-    parser.add_option( '-R', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable' )
-    parser.add_option( '-j', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments' )
-    parser.add_option( '-J', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments' )
-    parser.add_option( '-O', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand' )
-    parser.add_option( '-A', '--maxAlignAttempt', dest='maxAlignAttempt', help='Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate' )
-    parser.add_option( '-f', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand' )
-    parser.add_option( '-E', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand' )
-    parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' )
-    parser.add_option( '-S', '--seed', dest='seed', help='Seed for pseudo-random number generator' )
-    parser.add_option( '-8', '--snpphred', dest='snpphred', help='SNP penalty on Phred scale' )
-    parser.add_option( '-6', '--snpfrac', dest='snpfrac', help='Fraction of sites expected to be SNP sites' )
-    parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' )
-    parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' )
-    parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' )
-    parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' )
-    parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' )
-    parser.add_option( '-Y', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference' )
-    parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' )
-    parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' )
-    parser.add_option( '-y', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paired-end alignment' )
-    parser.add_option( '-z', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows' )
-    parser.add_option( '-W', '--iftab', dest='iftab', help='The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query' )
-    parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' )
-    parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' )
-    parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' )
-    parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index' )
-    parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' )
-    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
-    parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' )
-    parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' )
-    (options, args) = parser.parse_args()
-    stdout = ''
-
-    # make temp directory for placement of indices and copy reference file there if necessary
-    tmp_index_dir = tempfile.mkdtemp()
-    # get type of data (solid or solexa)
-    if options.dataType == 'solid':
-        colorspace = '-C'
-    else:
-        colorspace = ''
-    # index if necessary
-    if options.genomeSource == 'history' and not options.do_not_build_index:
-        # set up commands
-        if options.index_settings =='indexPreSet':
-            indexing_cmds = '%s' % colorspace
-        else:
-            try:
-                if options.iautoB and options.iautoB == 'set':
-                    iautoB = '--noauto'
-                else:
-                    iautoB = ''
-                if options. ipacked and options.ipacked == 'packed':
-                    ipacked = '--packed'
-                else:
-                    ipacked = ''
-                if options.ibmax and int( options.ibmax ) >= 1:
-                    ibmax = '--bmax %s' % options.ibmax
-                else:
-                    ibmax = ''
-                if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0:
-                    ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn
-                else:
-                    ibmaxdivn = ''
-                if options.idcv and int( options.idcv ) > 0:
-                    idcv = '--dcv %s' % options.idcv
-                else:
-                    idcv = ''
-                if options.inodc and options.inodc == 'nodc':
-                    inodc = '--nodc'
-                else:
-                    inodc = ''
-                if options.inoref and options.inoref == 'noref':
-                    inoref = '--noref'
-                else:
-                    inoref = ''
-                if options.iftab and int( options.iftab ) >= 0:
-                    iftab = '--ftabchars %s' % options.iftab
-                else:
-                    iftab = ''
-                if options.intoa and options.intoa == 'yes':
-                    intoa = '--ntoa'
-                else:
-                    intoa = ''
-                if options.iendian and options.iendian == 'big':
-                    iendian = '--big'
-                else:
-                    iendian = '--little'
-                if options.iseed and int( options.iseed ) > 0:
-                    iseed = '--seed %s' % options.iseed
-                else:
-                    iseed = ''
-                if options.icutoff and int( options.icutoff ) > 0:
-                    icutoff = '--cutoff %s' % options.icutoff
-                else:
-                    icutoff = ''
-                indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \
-                                ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,
-                                  inoref, options.ioffrate, iftab, intoa, iendian,
-                                  iseed, icutoff, colorspace )
-            except (ValueError, e):
-                # clean up temp dir
-                if os.path.exists( tmp_index_dir ):
-                    shutil.rmtree( tmp_index_dir )
-                stop_err( "Something is wrong with the indexing parameters and the indexing and alignment could not be run. Make sure you don't have any non-numeric values where they should be numeric.\n" + str( e ) )
-        ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
-        ref_file_name = ref_file.name
-        ref_file.close()
-        os.symlink( options.ref, ref_file_name )
-        cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name )
-        try:
-            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
-            tmp_stderr = open( tmp, 'wb' )
-            proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
-            returncode = proc.wait()
-            tmp_stderr.close()
-            # get stderr, allowing for case where it's very large
-            tmp_stderr = open( tmp, 'rb' )
-            stderr = ''
-            buffsize = 1048576
-            try:
-                while True:
-                    stderr += tmp_stderr.read( buffsize )
-                    if not stderr or len( stderr ) % buffsize != 0:
-                        break
-            except OverflowError:
-                pass
-            tmp_stderr.close()
-            if returncode != 0:
-                raise (Exception, stderr)
-        except Exception as e:
-            # clean up temp dir
-            if os.path.exists( tmp_index_dir ):
-                shutil.rmtree( tmp_index_dir )
-            stop_err( 'Error indexing reference sequence\n' + str( e ) )
-        stdout += 'File indexed. '
-    else:
-        ref_file_name = options.ref
-    # set up aligning and generate aligning command options
-    # automatically set threads in both cases
-    tmp_suppressed_file_name = None
-    tmp_unmapped_file_name = None
-    if options.suppressHeader == 'true':
-        suppressHeader = '--sam-nohead'
-    else:
-        suppressHeader = ''
-    if options.maxInsert and int( options.maxInsert ) > 0:
-        maxInsert = '-X %s' % options.maxInsert
-    else:
-        maxInsert = ''
-    if options.mateOrient:
-        mateOrient = '--%s' % options.mateOrient
-    else:
-        mateOrient = ''
-    quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING )
-    if options.params == 'preSet':
-        aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \
-                ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding )
-    else:
-        try:
-            if options.skip and int( options.skip ) > 0:
-                skip = '-s %s' % options.skip
-            else:
-                skip = ''
-            if options.alignLimit and int( options.alignLimit ) >= 0:
-                alignLimit = '-u %s' % options.alignLimit
-            else:
-                alignLimit = ''
-            if options.trimH and int( options.trimH ) > 0:
-                trimH = '-5 %s' % options.trimH
-            else:
-                trimH = ''
-            if options.trimL and int( options.trimL ) > 0:
-                trimL = '-3 %s' % options.trimL
-            else:
-                trimL = ''
-            if options.maqSoapAlign != '-1' and int( options.maqSoapAlign ) >= 0:
-                maqSoapAlign = '-v %s' % options.maqSoapAlign
-            else:
-                maqSoapAlign = ''
-            if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \
-                        or options.mismatchSeed == '2' or options.mismatchSeed == '3'):
-                mismatchSeed = '-n %s' % options.mismatchSeed
-            else:
-                mismatchSeed = ''
-            if options.mismatchQual and int( options.mismatchQual ) >= 0:
-                mismatchQual = '-e %s' % options.mismatchQual
-            else:
-                mismatchQual = ''
-            if options.seedLen and int( options.seedLen ) >= 5:
-                seedLen = '-l %s' % options.seedLen
-            else:
-                seedLen = ''
-            if options.rounding == 'noRound':
-                rounding = '--nomaqround'
-            else:
-                rounding = ''
-            if options.minInsert and int( options.minInsert ) > 0:
-                minInsert = '-I %s' % options.minInsert
-            else:
-                minInsert = ''
-            if options.maxAlignAttempt and int( options.maxAlignAttempt ) >= 0:
-                maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt
-            else:
-                maxAlignAttempt = ''
-            if options.forwardAlign == 'noForward':
-                forwardAlign = '--nofw'
-            else:
-                forwardAlign = ''
-            if options.reverseAlign == 'noReverse':
-                reverseAlign = '--norc'
-            else:
-                reverseAlign = ''
-            if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \
-                    ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ):
-                maxBacktracks = '--maxbts %s' % options.maxBacktracks
-            else:
-                maxBacktracks = ''
-            if options.tryHard == 'doTryHard':
-                tryHard = '-y'
-            else:
-                tryHard = ''
-            if options.valAlign and int( options.valAlign ) >= 0:
-                valAlign = '-k %s' % options.valAlign
-            else:
-                valAlign = ''
-            if options.allValAligns == 'doAllValAligns':
-                allValAligns = '-a'
-            else:
-                allValAligns = ''
-            if options.suppressAlign and int( options.suppressAlign ) >= 0:
-                suppressAlign = '-m %s' % options.suppressAlign
-            else:
-                suppressAlign = ''
-            if options.best == 'doBest':
-                best = '--best'
-            else:
-                best = ''
-            if options.strata == 'doStrata':
-                strata = '--strata'
-            else:
-                strata = ''
-            if options.offrate and int( options.offrate ) >= 0:
-                offrate = '-o %s' % options.offrate
-            else:
-                offrate = ''
-            if options.seed and int( options.seed ) >= 0:
-                seed = '--seed %s' % options.seed
-            else:
-                seed = ''
-            if options.paired == 'paired':
-                if options.output_unmapped_reads_l and options.output_unmapped_reads_r:
-                    tmp_unmapped_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
-                    tmp_unmapped_file_name = tmp_unmapped_file.name
-                    tmp_unmapped_file.close()
-                    output_unmapped_reads = '--un %s' % tmp_unmapped_file_name
-                else:
-                    output_unmapped_reads = ''
-                if options.output_suppressed_reads:
-                    tmp_suppressed_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
-                    tmp_suppressed_file_name = tmp_suppressed_file.name
-                    tmp_suppressed_file.close()
-                    output_suppressed_reads = '--max %s' % tmp_suppressed_file_name
-                else:
-                    output_suppressed_reads = ''
-            else:
-                if options.output_unmapped_reads:
-                    output_unmapped_reads = '--un %s' % options.output_unmapped_reads
-                else:
-                    output_unmapped_reads = ''
-                if options.output_suppressed_reads:
-                    output_suppressed_reads = '--max %s' % options.output_suppressed_reads
-                else:
-                    output_suppressed_reads = ''
-            snpfrac = ''
-            if options.snpphred and int( options.snpphred ) >= 0:
-                snpphred = '--snpphred %s' % options.snpphred
-            else:
-                snpphred = ''
-                if options.snpfrac and float( options.snpfrac ) >= 0:
-                    snpfrac = '--snpfrac %s' % options.snpfrac
-            if options.keepends and options.keepends == 'doKeepends':
-                keepends = '--col-keepends'
-            else:
-                keepends = ''
-            aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \
-                            '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
-                            ( maxInsert, mateOrient, options.threads, suppressHeader,
-                              colorspace, skip, alignLimit, trimH, trimL, maqSoapAlign,
-                              mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
-                              maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,
-                              tryHard, valAlign, allValAligns, suppressAlign, best,
-                              strata, offrate, seed, snpphred, snpfrac, keepends,
-                              output_unmapped_reads, output_suppressed_reads,
-                              quality_score_encoding )
-        except (ValueError):
-            # clean up temp dir
-            if os.path.exists( tmp_index_dir ):
-                shutil.rmtree( tmp_index_dir )
-            stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
-    try:
-        # have to nest try-except in try-finally to handle 2.4
-        try:
-            # prepare actual mapping commands
-            if options.paired == 'paired':
-                cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
-            else:
-                cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
-            # align
-            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
-            tmp_stderr = open( tmp, 'wb' )
-            proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
-            returncode = proc.wait()
-            tmp_stderr.close()
-            # get stderr, allowing for case where it's very large
-            tmp_stderr = open( tmp, 'rb' )
-            stderr = ''
-            buffsize = 1048576
-            try:
-                while True:
-                    stderr += tmp_stderr.read( buffsize )
-                    if not stderr or len( stderr ) % buffsize != 0:
-                        break
-            except OverflowError:
-                pass
-            tmp_stderr.close()
-            if returncode != 0:
-                raise (Exception, stderr)
-            # get suppressed and unmapped reads output files in place if appropriate
-            if options.paired == 'paired' and tmp_suppressed_file_name and \
-                               options.output_suppressed_reads_l and options.output_suppressed_reads_r:
-                try:
-                    left = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
-                    right = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
-                    shutil.move( left, options.output_suppressed_reads_l )
-                    shutil.move( right, options.output_suppressed_reads_r )
-                except Exception as e:
-                    sys.stdout.write( 'Error producing the suppressed output file.\n' )
-            if options.paired == 'paired' and tmp_unmapped_file_name and \
-                               options.output_unmapped_reads_l and options.output_unmapped_reads_r:
-                try:
-                    left = tmp_unmapped_file_name.replace( '.fastq', '_1.fastq' )
-                    right = tmp_unmapped_file_name.replace( '.fastq', '_2.fastq' )
-                    shutil.move( left, options.output_unmapped_reads_l )
-                    shutil.move( right, options.output_unmapped_reads_r )
-                except Exception as e:
-                    sys.stdout.write( 'Error producing the unmapped output file.\n' )
-            # check that there are results in the output file
-            if os.path.getsize( options.output ) == 0:
-                raise (Exception, 'The output file is empty, there may be an error with your input file or settings.')
-        except Exception as e:
-            stop_err( 'Error aligning sequence. ' + str( e ) )
-    finally:
-        # clean up temp dir
-        if os.path.exists( tmp_index_dir ):
-            shutil.rmtree( tmp_index_dir )
-    stdout += 'Sequence file aligned.\n'
-    sys.stdout.write( stdout )
-
-if __name__=="__main__": __main__()
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in2.fastqsanger	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-@HWI-EAS91_1_30788AAXX:1:1:1513:715/1
-GTTTTTTGGGCATAGATGTTTAGTTGTGGTAGTCAG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I
-@HWI-EAS91_1_30788AAXX:1:1:1698:516/1
-GTTGTTAGGGAGAGGAGTTGAACCTCTGAGTGTAAA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIII5IIIII9I
-@HWI-EAS91_1_30788AAXX:1:1:1491:637/1
-GCTAGCAGGATGGATCCGGCAATTGGGGCTTCTACA
-+
-IIIIIII""IIIIIIIIIIIIFIIIIIIIIIIIABD
-@HWI-EAS91_1_30788AAXX:1:1:1711:249/1
-GGAAGTAGGGGCCTGCGTTCAGGCGTTCTGTTTGGT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII
-@HWI-EAS91_1_30788AAXX:1:1:1634:211/1
-GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF
-@HWI-EAS91_1_30788AAXX:1:1:1218:141/1
-GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I
-@HWI-EAS91_1_30788AAXX:1:1:1398:854/1
-GTGAAGAGGAGGGGATTTATTAGTACGGGAAGGGTG
-+
-IIIIIII""IIIIIBIIIIIIIIIIIIIIA=IIIII
-@HWI-EAS91_1_30788AAXX:1:1:1310:991/1
-GAATAGTGGTAGTATTATTCCTTCTAGGCATAGGAG
-+
-IIIIIII""IIIIIIIIII4IIIIIIDII:IEI2:I
-@HWI-EAS91_1_30788AAXX:1:1:1716:413/1
-GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII
-@HWI-EAS91_1_30788AAXX:1:1:1630:59/1
-GGAGCGGGGGGTTGGTAAGGTTGGGGTCGAGTATGA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIII;IIHIIF
-@HWI-EAS91_1_30788AAXX:1:1:1601:805/1
-GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III
-@HWI-EAS91_1_30788AAXX:1:1:1663:724/1
-GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA
-+
-IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3
-@HWI-EAS91_1_30788AAXX:1:1:1454:975/1
-GCTAGGCGGGAGTGGTAAAAGGCTCAGAAGAAGCCA
-+
-IIIIIII""IIIIIIIIIIIIIIIIEIG;IIIIIII
-@HWI-EAS91_1_30788AAXX:1:1:1461:255/1
-GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT
-+
-IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I
-@HWI-EAS91_1_30788AAXX:1:1:1775:764/1
-GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC
-+
-IIIIIII""III@IIII+IIIIII8H8IIIIIIICI
-@HWI-EAS91_1_30788AAXX:1:1:1269:520/1
-GGAGTATGGAATAAGTGATTTTAGATCGGTTTGTCG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII
-@HWI-EAS91_1_30788AAXX:1:1:1303:1162/1
-GAGCAAGGGCAGGAGGAGGAGTCCTAGGATGTCTTT
-+
-IIIIIII""IIIIFII4*IGIAI(IAII49',3I6I
-@HWI-EAS91_1_30788AAXX:1:1:1090:409/1
-GTTTGTTGGGAATGGAGCGTAGGATGGCGTAGGCAA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIII:IIA8I
-@HWI-EAS91_1_30788AAXX:1:1:1336:1000/1
-GGTAAATGGGAAATATTAAGTTTCTGTTTCTAGATC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIII9II
-@HWI-EAS91_1_30788AAXX:1:1:1199:1376/1
-GTTTTCTGGAAAACCTTCACCTATTTATGGGGGTTT
-+
-IIIIIII""IIIIIIIIIIIII;III3IIG&:/III
-@HWI-EAS91_1_30788AAXX:1:1:1598:1148/1
-GATCAATGGTTTGGATCAATAAGTGATTATATATTT
-+
-IIIIIII""IIIIIDIIIIII?IIICII=IHIIIII
-@HWI-EAS91_1_30788AAXX:1:1:1723:1459/1
-GAAACCCGGACGTTTGGATGGGCCCGGAGCGAGGAT
-+
-IIIIIII""IIIIIIIIDIIIIIIIII9HII-II=I
-@HWI-EAS91_1_30788AAXX:1:1:1442:1346/1
-TATCAAGGGGCTGCTTCGAATCCGAAGTGGTGGCTG
-+
-IIIIIII""IIIIIDIIIII1I(I4II<?<-II*,&
-@HWI-EAS91_1_30788AAXX:1:1:850:117/1
-GTATGACGGTAAAGAAAATTATTACGAATGCATGGG
-+
-IIIIIII""IIIIIIEIEIIIIIIIIEBIDD9I;:?
-@HWI-EAS91_1_30788AAXX:1:1:795:325/1
-GGGTACTGGGAAGTGGAATGGTGTGAGTCCAAGTTT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIII65IIII
-@HWI-EAS91_1_30788AAXX:1:1:873:453/1
-GAGTAGGGGGATTGCTAGAGTTACTTCGTATGAGAT
-+
-IIIIIII""IIIIIIIIIIIIIIIII@IIIIIII=I
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in5.fastqillumina	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/1
-TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA
-+
-hhhhhhhAAhhhhhhhhhhh^hOhhhhghhhfhhhhhOhh^hAAhhhhhh
-@Dummy:1:1:1578:331/1
-TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1647:512/1
-TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1570:620/1
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-+
-hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1599:330/1
-AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhh[hhh_hhAhhhhhhhOOOhhhh
-@Dummy:1:1:1652:270/1
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1746:351/1
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1582:633/1
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1598:534/1
-GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1572:324/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOThAhhhhhhhOOOhhhh
-@Dummy:1:1:1749:466/1
-TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1629:446/1
-AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1763:587/1
-AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1616:363/1
-TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhchhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1768:715/1
-ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT
-+
-hhhhhhhAAhhhhhhhhhhhhhchhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1572:270/1
-TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1673:514/1
-ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhPAhhhhhhhOOOhhhh
-@Dummy:1:1:1634:330/1
-GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhWhhAhhhhhhhOOOhhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in5.fastqsanger	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/1
-TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA
-+
-IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII
-@Dummy:1:1:1578:331/1
-TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1647:512/1
-TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1570:620/1
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-+
-IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1599:330/1
-AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII
-@Dummy:1:1:1652:270/1
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII
-@Dummy:1:1:1746:351/1
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1582:633/1
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1598:534/1
-GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1572:324/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII
-@Dummy:1:1:1749:466/1
-TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1629:446/1
-AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1763:587/1
-AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1616:363/1
-TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII
-@Dummy:1:1:1768:715/1
-ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT
-+
-IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1572:270/1
-TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1673:514/1
-ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII
-@Dummy:1:1:1634:330/1
-GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in5.fastqsolexa	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/1
-TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA
-+
-hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhhhOhh^h;;hhhhhh
-@Dummy:1:1:1578:331/1
-TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1647:512/1
-TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1570:620/1
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-+
-hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1599:330/1
-AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhh[hhh_hh;hhhhhhhOOOhhhh
-@Dummy:1:1:1652:270/1
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1746:351/1
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1582:633/1
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1598:534/1
-GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1572:324/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh;hhhhhhhOOOhhhh
-@Dummy:1:1:1749:466/1
-TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1629:446/1
-AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1763:587/1
-AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1616:363/1
-TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhchhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1768:715/1
-ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT
-+
-hhhhhhh;;hhhhhhhhhhhhhchhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1572:270/1
-TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1673:514/1
-ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhP;hhhhhhhOOOhhhh
-@Dummy:1:1:1634:330/1
-GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhWhh;hhhhhhhOOOhhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in6.fastqillumina	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/2
-TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG
-+
-hhhhhhhAAhhhhhhhOhh^hAAhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1578:331/2
-AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1647:512/2
-TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1570:620/2
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-+
-hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1599:330/2
-TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhh[hhh_hh^hOhhhhghhhfhhh
-@Dummy:1:1:1652:270/2
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh
-@Dummy:1:1:1582:633/2
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1598:534/2
-TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1572:324/2
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh
-@Dummy:1:1:1749:466/2
-GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1629:446/2
-CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1763:587/2
-CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1616:363/2
-GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhchhh^hOhhhhghhhfhhh
-@Dummy:1:1:1768:715/2
-AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA
-+
-hhhhhhhAAhhhhhhhhhhhhhchhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1572:270/2
-ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1673:514/2
-GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhP^hOhhhhghhhfhhh
-@Dummy:1:1:1634:330/2
-TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhWhh^hOhhhhghhhfhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in6.fastqsanger	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/2
-TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG
-+
-IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1578:331/2
-AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1647:512/2
-TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1570:620/2
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-+
-IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1599:330/2
-TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII
-@Dummy:1:1:1652:270/2
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-+
-IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII
-@Dummy:1:1:1582:633/2
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1598:534/2
-TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1572:324/2
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII
-@Dummy:1:1:1749:466/2
-GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1629:446/2
-CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1763:587/2
-CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1616:363/2
-GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII
-@Dummy:1:1:1768:715/2
-AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA
-+
-IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1572:270/2
-ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1673:514/2
-GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII
-@Dummy:1:1:1634:330/2
-TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in6.fastqsolexa	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/2
-TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG
-+
-hhhhhhh;;hhhhhhhOhh^h;;hhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1578:331/2
-AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1647:512/2
-TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1570:620/2
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-+
-hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1599:330/2
-TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhh[hhh_hh^hOhhhhghhhfhhh
-@Dummy:1:1:1652:270/2
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh
-@Dummy:1:1:1582:633/2
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1598:534/2
-TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1572:324/2
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh
-@Dummy:1:1:1749:466/2
-GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1629:446/2
-CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1763:587/2
-CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1616:363/2
-GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhchhh^hOhhhhghhhfhhh
-@Dummy:1:1:1768:715/2
-AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA
-+
-hhhhhhh;;hhhhhhhhhhhhhchhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1572:270/2
-ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1673:514/2
-GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhP^hOhhhhghhhfhhh
-@Dummy:1:1:1634:330/2
-TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhWhh^hOhhhhghhhfhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out10.sam	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-Dummy:1:1:1570:620	141	*	0	0	*	*	0	0	CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1570:620	77	*	0	0	*	*	0	0	GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1572:270	131	phiX174	3577	255	50M	=	3518	-109	ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1572:270	67	phiX174	3518	255	50M	=	3577	109	TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1572:324	141	*	0	0	*	*	0	0	GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1572:324	77	*	0	0	*	*	0	0	AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1578:331	131	phiX174	268	255	50M	=	209	-109	AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1578:331	67	phiX174	209	255	50M	=	268	109	TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1582:633	141	*	0	0	*	*	0	0	TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1582:633	77	*	0	0	*	*	0	0	CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1598:534	131	phiX174	1772	255	50M	=	1717	-105	TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1598:534	67	phiX174	1717	255	50M	=	1772	105	GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1599:330	131	phiX174	868	255	50M	=	803	-115	TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1599:330	67	phiX174	803	255	50M	=	868	115	AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1616:363	131	phiX174	2773	255	50M	=	2718	-105	GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1616:363	67	phiX174	2718	255	50M	=	2773	105	TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1629:446	131	phiX174	2355	255	50M	=	2301	-104	CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1629:446	67	phiX174	2301	255	50M	=	2355	104	AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1634:330	131	phiX174	4473	255	50M	=	4418	-105	TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1634:330	67	phiX174	4418	255	50M	=	4473	105	GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1647:512	131	phiX174	451	255	50M	=	401	-100	TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1647:512	67	phiX174	401	255	50M	=	451	100	TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1652:270	141	*	0	0	*	*	0	0	GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1652:270	77	*	0	0	*	*	0	0	AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1673:514	131	phiX174	4072	255	50M	=	4018	-104	GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1673:514	67	phiX174	4018	255	50M	=	4072	104	ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1746:351	141	*	0	0	*	*	0	0	CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT	IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII	XM:i:0
-Dummy:1:1:1746:351	77	*	0	0	*	*	0	0	CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1749:466	131	phiX174	2251	255	50M	=	2201	-100	GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1749:466	67	phiX174	2201	255	50M	=	2251	100	TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1761:343	131	phiX174	69	255	50M	=	5	-114	TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG	IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1761:343	67	phiX174	5	255	50M	=	69	114	TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA	IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1763:587	131	phiX174	2566	255	50M	=	2501	-115	CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1763:587	67	phiX174	2501	255	50M	=	2566	115	AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1768:715	131	phiX174	3173	255	50M	=	3118	-105	AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1768:715	67	phiX174	3118	255	50M	=	3173	105	ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out6.sam	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-HWI-EAS91_1_30788AAXX:1:1:1090:409/1	16	chrM	15014	255	36M	*	0	0	TTGCCTACGCCATCCTACGCTCCATTCCCAACAAAC	I8AII:IIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1199:1376/1	16	chrM	14023	255	36M	*	0	0	AAACCCCCATAAATAGGTGAAGGTTTTCCAGAAAAC	III/:&GII3III;IIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27G0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1218:141/1	4	*	0	0	*	*	0	0	GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG	IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I	XM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1269:520/1	16	chrM	11036	255	36M	*	0	0	CGACAAACCGATCTAAAATCACTTATTCCATACTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27G8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1303:1162/1	16	chrM	14866	255	36M	*	0	0	AAAGACATCCTAGGACTCCTCCTCCTGCCCTTGCTC	I6I3,'94IIAI(IAIGI*4IIFIIII""IIIIIII	XA:i:2	MD:Z:27A0T7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1310:991/1	16	chrM	10002	255	36M	*	0	0	CTCCTATGCCTAGAAGGAATAATACTACCACTATTC	I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1336:1000/1	16	chrM	11616	255	36M	*	0	0	GATCTAGAAACAGAAACTTAATATTTCCCATTTACC	II9IIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27T0T7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1398:854/1	16	chrM	3921	255	36M	*	0	0	CACCCTTCCCGTACTAATAAATCCCCTCCTCTTCAC	IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII	XA:i:2	MD:Z:27T0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1442:1346/1	16	chrM	9331	255	36M	*	0	0	CAGCCACCACTTCGGATTCGAAGCAGCCCCTTGATA	&,*II-<?<II4I(I1IIIIIDIIIII""IIIIIII	XA:i:1	MD:Z:28G7	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1454:975/1	16	chrM	8929	255	36M	*	0	0	TGGCTTCTTCTGAGCCTTTTACCACTCCCGCCTAGC	IIIIIII;GIEIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1461:255/1	0	chrM	12988	255	36M	*	0	0	GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT	IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I	XA:i:2	MD:Z:7A0A27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1491:637/1	16	chrM	10864	255	36M	*	0	0	TGTAGAAGCCCCAATTGCCGGATCCATCCTGCTAGC	DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1513:715/1	16	chrM	9563	255	36M	*	0	0	CTGACTACCACAACTAAACATCTATGCCCAAAAAAC	I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1598:1148/1	16	chrM	2334	255	36M	*	0	0	AAATATATAATCACTTATTGATCCAAACCATTGATC	IIIIIHI=IICIII?IIIIIIDIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1601:805/1	0	chrM	12584	255	36M	*	0	0	GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III	XA:i:2	MD:Z:7A0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1630:59/1	16	chrM	12387	255	36M	*	0	0	TCATACTCGACCCCAACCTTACCAACCCCCCGCTCC	FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1634:211/1	0	chrM	9350	255	36M	*	0	0	GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF	XA:i:2	MD:Z:7C0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1663:724/1	0	chrM	15012	255	36M	*	0	0	GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA	IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3	XA:i:2	MD:Z:7T0A27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1698:516/1	16	chrM	2735	255	36M	*	0	0	TTTACACTCAGAGGTTCAACTCCTCTCCCTAACAAC	I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1711:249/1	16	chrM	10617	255	36M	*	0	0	ACCAAACAGAACGCCTGAACGCAGGCCCCTACTTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1716:413/1	0	chrM	6040	255	36M	*	0	0	GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII	XA:i:2	MD:Z:7T0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1723:1459/1	16	chrM	15787	255	36M	*	0	0	ATCCTCGCTCCGGGCCCATCCAAACGTCCGGGTTTC	I=II-IIH9IIIIIIIIIDIIIIIIII""IIIIIII	XA:i:2	MD:Z:27G0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1775:764/1	0	chrM	16613	255	36M	*	0	0	GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC	IIIIIII""III@IIII+IIIIII8H8IIIIIIICI	XA:i:2	MD:Z:7C0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:795:325/1	16	chrM	4249	255	36M	*	0	0	AAACTTGGACTCACACCATTCCACTTCCCAGTACCC	IIII56IIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27T0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:850:117/1	16	chrM	5540	255	36M	*	0	0	CCCATGCATTCGTAATAATTTTCTTTACCGTCATAC	?:;I9DDIBEIIIIIIIIEIEIIIIII""IIIIIII	XA:i:2	MD:Z:27T0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:873:453/1	16	chrM	3188	255	36M	*	0	0	ATCTCATACGAAGTAACTCTAGCAATCCCCCTACTC	I=IIIIIII@IIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0T7	NM:i:2
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out7.sam	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-Dummy:1:1:1570:620	141	*	0	0	*	*	0	0	CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1570:620	77	*	0	0	*	*	0	0	GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1572:270	131	phiX174	3577	255	50M	=	3518	-109	ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1572:270	67	phiX174	3518	255	50M	=	3577	109	TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1572:324	141	*	0	0	*	*	0	0	GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1572:324	77	*	0	0	*	*	0	0	AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1578:331	131	phiX174	268	255	50M	=	209	-109	AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1578:331	67	phiX174	209	255	50M	=	268	109	TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1582:633	141	*	0	0	*	*	0	0	TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1582:633	77	*	0	0	*	*	0	0	CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1598:534	131	phiX174	1772	255	50M	=	1717	-105	TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1598:534	67	phiX174	1717	255	50M	=	1772	105	GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1599:330	131	phiX174	868	255	50M	=	803	-115	TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1599:330	67	phiX174	803	255	50M	=	868	115	AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1616:363	131	phiX174	2773	255	50M	=	2718	-105	GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1616:363	67	phiX174	2718	255	50M	=	2773	105	TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1629:446	131	phiX174	2355	255	50M	=	2301	-104	CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1629:446	67	phiX174	2301	255	50M	=	2355	104	AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1634:330	131	phiX174	4473	255	50M	=	4418	-105	TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1634:330	67	phiX174	4418	255	50M	=	4473	105	GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1647:512	131	phiX174	451	255	50M	=	401	-100	TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1647:512	67	phiX174	401	255	50M	=	451	100	TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1652:270	141	*	0	0	*	*	0	0	GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1652:270	77	*	0	0	*	*	0	0	AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1673:514	131	phiX174	4072	255	50M	=	4018	-104	GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1673:514	67	phiX174	4018	255	50M	=	4072	104	ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1746:351	141	*	0	0	*	*	0	0	CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT	IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII	XM:i:0
-Dummy:1:1:1746:351	77	*	0	0	*	*	0	0	CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1749:466	131	phiX174	2251	255	50M	=	2201	-100	GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1749:466	67	phiX174	2201	255	50M	=	2251	100	TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1761:343	131	phiX174	69	255	50M	=	5	-114	TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG	IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1761:343	67	phiX174	5	255	50M	=	69	114	TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA	IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1763:587	131	phiX174	2566	255	50M	=	2501	-115	CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1763:587	67	phiX174	2501	255	50M	=	2566	115	AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1768:715	131	phiX174	3173	255	50M	=	3118	-105	AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1768:715	67	phiX174	3118	255	50M	=	3173	105	ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_1.fastq	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/1
-@Dummy:1:1:1572:324/1
-@Dummy:1:1:1582:633/1
-@Dummy:1:1:1652:270/1
-@Dummy:1:1:1746:351/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII
-IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_1.fastqillumina.sorted	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/1
-@Dummy:1:1:1572:324/1
-@Dummy:1:1:1582:633/1
-@Dummy:1:1:1652:270/1
-@Dummy:1:1:1746:351/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhhAhhhhhhhOOOhhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOThAhhhhhhhOOOhhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhhAhhhhhhhOOOhhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_1.fastqsolexa.sorted	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/1
-@Dummy:1:1:1572:324/1
-@Dummy:1:1:1582:633/1
-@Dummy:1:1:1652:270/1
-@Dummy:1:1:1746:351/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh;hhhhhhhOOOhhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh;hhhhhhhOOOhhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh;hhhhhhhOOOhhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_2.fastq	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/2
-@Dummy:1:1:1572:324/2
-@Dummy:1:1:1582:633/2
-@Dummy:1:1:1652:270/2
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII
-IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII
-IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_2.fastqillumina.sorted	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/2
-@Dummy:1:1:1572:324/2
-@Dummy:1:1:1582:633/2
-@Dummy:1:1:1652:270/2
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
-hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_2.fastqsolexa.sorted	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/2
-@Dummy:1:1:1572:324/2
-@Dummy:1:1:1582:633/2
-@Dummy:1:1:1652:270/2
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
-hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out9.sam	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-HWI-EAS91_1_30788AAXX:1:1:1090:409/1	16	chrM	15014	255	36M	*	0	0	TTGCCTACGCCATCCTACGCTCCATTCCCAACAAAC	I8AII:IIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1199:1376/1	16	chrM	14023	255	36M	*	0	0	AAACCCCCATAAATAGGTGAAGGTTTTCCAGAAAAC	III/:&GII3III;IIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27G0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1218:141/1	4	*	0	0	*	*	0	0	GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG	IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I	XM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1269:520/1	16	chrM	11036	255	36M	*	0	0	CGACAAACCGATCTAAAATCACTTATTCCATACTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27G8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1303:1162/1	16	chrM	14866	255	36M	*	0	0	AAAGACATCCTAGGACTCCTCCTCCTGCCCTTGCTC	I6I3,'94IIAI(IAIGI*4IIFIIII""IIIIIII	XA:i:2	MD:Z:27A0T7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1310:991/1	16	chrM	10002	255	36M	*	0	0	CTCCTATGCCTAGAAGGAATAATACTACCACTATTC	I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1336:1000/1	16	chrM	11616	255	36M	*	0	0	GATCTAGAAACAGAAACTTAATATTTCCCATTTACC	II9IIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27T0T7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1398:854/1	16	chrM	3921	255	36M	*	0	0	CACCCTTCCCGTACTAATAAATCCCCTCCTCTTCAC	IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII	XA:i:2	MD:Z:27T0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1442:1346/1	16	chrM	9331	255	36M	*	0	0	CAGCCACCACTTCGGATTCGAAGCAGCCCCTTGATA	&,*II-<?<II4I(I1IIIIIDIIIII""IIIIIII	XA:i:1	MD:Z:28G7	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1454:975/1	16	chrM	8929	255	36M	*	0	0	TGGCTTCTTCTGAGCCTTTTACCACTCCCGCCTAGC	IIIIIII;GIEIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1461:255/1	0	chrM	12988	255	36M	*	0	0	GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT	IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I	XA:i:2	MD:Z:7A0A27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1491:637/1	16	chrM	10864	255	36M	*	0	0	TGTAGAAGCCCCAATTGCCGGATCCATCCTGCTAGC	DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1513:715/1	16	chrM	9563	255	36M	*	0	0	CTGACTACCACAACTAAACATCTATGCCCAAAAAAC	I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1598:1148/1	16	chrM	2334	255	36M	*	0	0	AAATATATAATCACTTATTGATCCAAACCATTGATC	IIIIIHI=IICIII?IIIIIIDIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1601:805/1	0	chrM	12584	255	36M	*	0	0	GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III	XA:i:2	MD:Z:7A0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1630:59/1	16	chrM	12387	255	36M	*	0	0	TCATACTCGACCCCAACCTTACCAACCCCCCGCTCC	FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1634:211/1	0	chrM	9350	255	36M	*	0	0	GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF	XA:i:2	MD:Z:7C0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1663:724/1	0	chrM	15012	255	36M	*	0	0	GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA	IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3	XA:i:2	MD:Z:7T0A27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1698:516/1	16	chrM	2735	255	36M	*	0	0	TTTACACTCAGAGGTTCAACTCCTCTCCCTAACAAC	I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1711:249/1	16	chrM	10617	255	36M	*	0	0	ACCAAACAGAACGCCTGAACGCAGGCCCCTACTTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1716:413/1	0	chrM	6040	255	36M	*	0	0	GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII	XA:i:2	MD:Z:7T0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1723:1459/1	16	chrM	15787	255	36M	*	0	0	ATCCTCGCTCCGGGCCCATCCAAACGTCCGGGTTTC	I=II-IIH9IIIIIIIIIDIIIIIIII""IIIIIII	XA:i:2	MD:Z:27G0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1775:764/1	0	chrM	16613	255	36M	*	0	0	GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC	IIIIIII""III@IIII+IIIIII8H8IIIIIIICI	XA:i:2	MD:Z:7C0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:795:325/1	16	chrM	4249	255	36M	*	0	0	AAACTTGGACTCACACCATTCCACTTCCCAGTACCC	IIII56IIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27T0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:850:117/1	16	chrM	5540	255	36M	*	0	0	CCCATGCATTCGTAATAATTTTCTTTACCGTCATAC	?:;I9DDIBEIIIIIIIIEIEIIIIII""IIIIIII	XA:i:2	MD:Z:27T0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:873:453/1	16	chrM	3188	255	36M	*	0	0	ATCTCATACGAAGTAACTCTAGCAATCCCCCTACTC	I=IIIIIII@IIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0T7	NM:i:2
--- a/bowtie_remove_rrna_wrapper/test-data/phiX.fasta	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
->phiX174
-GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
-GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
-ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
-TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
-GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
-TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
-TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
-CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
-TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
-TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
-GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
-CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
-TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
-AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
-CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
-TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
-TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
-CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
-GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
-GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
-ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
-TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
-TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
-ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
-CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
-GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
-CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
-TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
-TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
-TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
-AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
-TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
-ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
-GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
-TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
-TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
-TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
-TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
-CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
-AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
-CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
-TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
-CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
-AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
-GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
-GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
-TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
-CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
-TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
-GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
-CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
-TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
-AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
-TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
-CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
-TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
-TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
-CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
-TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
-ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
-TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
-ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
-GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
-CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
-GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
-GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
-ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
-CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
-CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
-GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
-CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
-CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
-TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
-TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
-TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
-AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
-TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
-
--- a/bowtie_remove_rrna_wrapper/tool-data/bowtie_indices.loc	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Mouse_rRNA	Mouse_rRNA	Mouse_rRNA	/home/DATA/galaxy/galaxy-dist/data/indexes/bowtie_rrna_indexes/Mouse_rRNA/bowtie_rrna_indexes/mouse_rRNA_index
--- a/bowtie_remove_rrna_wrapper/tool_data_table_conf.xml.sample	Wed Feb 23 13:57:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<tables>
-    <!-- Locations of indexes in the Bowtie mapper format -->
-    <table name="bowtie_rrna_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices.loc" />
-    </table>
-</tables>
-