Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna
diff bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml @ 21:b49ad9f12dfa draft
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| author | jackcurragh |
|---|---|
| date | Wed, 11 May 2022 13:37:35 +0000 |
| parents | dbb3e98144fd |
| children | ca7c965f7cc9 |
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--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml Wed Apr 13 09:00:19 2022 +0000 +++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml Wed May 11 13:37:35 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="bowtie_rRNA_tRNA_removal_wrapper" name="Remove rRNA and tRNA using Bowtie" version="1.4.0"> +<tool id="bowtie_rRNA_tRNA_removal_wrapper" name="Remove rRNA and tRNA using Bowtie" version="1.5.0"> <description></description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -156,11 +156,11 @@ <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" selected="True">Use one from the history</option> + <option value="history">Use one from the history</option> </param> <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_data_table="bowtie_indexes"> + <param name="index" type="select" label="Select a reference index" help="if your index of interest is not listed - contact Galaxy team"> + <options from_data_table="bowtie_rRNA_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> @@ -256,8 +256,8 @@ <option value="noForward">Do not align against the forward reference strand</option> </param> <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)"> - <option value="reverse">Align against the reverse-complement reference strand</option> - <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option> + <option value="reverse" selected="true">Align against the reverse-complement reference strand</option> + <option value="noReverse">Do not align against the reverse-complement reference strand</option> </param> <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"> @@ -352,7 +352,7 @@ </param> </when> <when value="vMode"> - <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" /> + <param name="maxMismatches" type="integer" value="3" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" /> <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" /> </when> </conditional> @@ -362,8 +362,8 @@ <option value="noForward">Do not align against the forward reference strand</option> </param> <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)"> - <option value="reverse">Align against the reverse-complement reference strand</option> - <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option> + <option value="reverse" selected='true'>Align against the reverse-complement reference strand</option> + <option value="noReverse">Do not align against the reverse-complement reference strand</option> </param> <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"> @@ -420,16 +420,18 @@ </conditional> <!-- pParams --> </when> <!-- paired --> </conditional> <!-- singlePaired --> + <param name="save_mapped_reads" type="boolean" checked="False" label="Same the bowtie alignments to the non-coding RNA" /> <param name="save_mapping_stats" type="boolean" checked="True" label="Save the bowtie mapping statistics to the history" /> <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" 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"> + <filter>save_mapped_reads is True</filter> <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"> + <option type="from_data_table" name="bowtie_rRNA_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> @@ -540,254 +542,15 @@ </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"> - <metadata name="dbkey" value="equCab2" /> - </output> - </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="alignMode" value="nMode" /> - <param name="pMismatchSeed" value="2" /> - <param name="pMismatchQual" value="70" /> - <param name="pSeedLen" value="28" /> - <param name="pRounding" value="round" /> - <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="alignMode" value="nMode" /> - <param name="pMismatchSeed" value="2" /> - <param name="pMismatchQual" value="70" /> - <param name="pSeedLen" value="28" /> - <param name="pRounding" value="round" /> - <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="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" /> - <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" /> - </test> - <test> - <param name="genomeSource" value="history" /> - <param name="ownFile" value="phiX.fasta" /> + <param name="ownFile" value="chr9_100000bases.fa" /> <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="alignMode" value="nMode" /> - <param name="pMismatchSeed" value="2" /> - <param name="pMismatchQual" value="70" /> - <param name="pSeedLen" value="28" /> - <param name="pRounding" value="round" /> - <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" /> + <param name="sPaired" value="single" /> + <param name="sInput1" ftype="fastqsanger" value="test.fastq" /> + <param name="alignMode" value="vMode" /> + <output name="output_unmapped_reads_l" ftype="fastqsanger" file="lesschr9.fastq" /> </test> - <!-- end testing of non-sanger variant fastq reads --> - <test> - <!-- - Bowtie command: - bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 -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="alignMode" value="nMode" /> - <param name="sMismatchSeed" value="2" /> - <param name="sMismatchQual" value="70" /> - <param name="sSeedLen" value="28" /> - <param name="sRounding" value="round" /> - <param name="sForwardAlign" value="forward" /> - <param name="sReverseAlign" value="reverse" /> - <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="sOffrate" value="-1" /> - <param name="sSeed" value="-1" /> - <param name="suppressHeader" value="true" /> - <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True"> - <metadata name="dbkey" value="equCab2" /> - </output> - </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="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> - <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="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" /> - <param name="save_mapping_stats" value="true" /> - <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" /> - <output name="mapping_stats" ftype="txt" file="bowtie_out11.txt" sort="True" /> - </test> + </tests> <help>