Mercurial > repos > devteam > bowtie_wrappers
diff bowtie_wrapper.xml @ 5:306077e393d4 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit b2e1043bf4db38be490fec298a1829f8e4a1c48e
author | devteam |
---|---|
date | Thu, 18 Aug 2016 10:20:09 -0400 |
parents | df86f29bedee |
children | ecbbc8be6266 |
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--- a/bowtie_wrapper.xml Tue Jul 21 13:04:45 2015 -0400 +++ b/bowtie_wrapper.xml Thu Aug 18 10:20:09 2016 -0400 @@ -1,6 +1,6 @@ -<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.3"> +<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.5"> <requirements> - <requirement type="package" version="0.12.7">bowtie</requirement> + <requirement type="package" version="1.1.2">bowtie</requirement> </requirements> <description></description> <version_command>bowtie --version</version_command> @@ -148,6 +148,9 @@ --seed="${singlePaired.pParams.pSeed}" #end if #end if + #if $save_mapping_stats + --output_mapping_stats="$mapping_stats" + #end if </command> <inputs> <conditional name="refGenomeSource"> @@ -415,6 +418,7 @@ </conditional> <!-- pParams --> </when> <!-- paired --> </conditional> <!-- singlePaired --> + <param name="save_mapping_stats" type="boolean" checked="False" 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> @@ -437,6 +441,9 @@ </conditional> </actions> </data> + <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats"> + <filter>save_mapping_stats is True</filter> + </data> <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> <filter>(( singlePaired['sPaired'] == "single" and @@ -545,7 +552,9 @@ <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" /> + <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True"> + <metadata name="dbkey" value="equCab2" /> + </output> </test> <test> <!-- @@ -713,7 +722,9 @@ <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" /> + <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True"> + <metadata name="dbkey" value="equCab2" /> + </output> </test> <test> <!-- @@ -744,6 +755,37 @@ <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>