Mercurial > repos > cmonjeau > stacks
diff STACKS_procrad.xml @ 0:d6ba40f6c824
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| author | cmonjeau |
|---|---|
| date | Mon, 24 Aug 2015 09:29:12 +0000 |
| parents | |
| children | c9e10e0d6c10 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/STACKS_procrad.xml Mon Aug 24 09:29:12 2015 +0000 @@ -0,0 +1,382 @@ +<?xml version="1.0"?> +<tool id="STACKSprocrad" name="STACKS : Process radtags" force_history_refresh="True" version="1.1.0"> +<description>Run the STACKS cleaning script</description> +<configfiles> +<configfile name="input_single"> +#if str( $options_type.options_type_selector ) == "single": +#for $input in $options_type.inputs_single: +${input.display_name}::${input} +#end for +#end if +</configfile> +<configfile name="input_paired1"> +#if str( $options_type.options_type_selector ) == "paired": +#for $input in $options_type.inputs_paired1: +${input.display_name}::${input} +#end for +#end if +</configfile> +<configfile name="input_paired2"> +#if str( $options_type.options_type_selector ) == "paired": +#for $input in $options_type.inputs_paired2: +${input.display_name}::${input} +#end for +#end if +</configfile> +</configfiles> +<requirements> + <requirement type="package" version="1.18">stacks</requirement> + </requirements> +<command interpreter="python"> + +STACKS_procrad.py + --input_type $options_type.options_type_selector + #if str( $options_type.options_type_selector ) == "single": + --input_single $input_single + #else + --input_paired1 $input_paired1 + --input_paired2 $input_paired2 + #end if + --inputype $inputype + --barcode $barcode + --sample_name $sample_name + --output_choice $options_output_infos_selector + #if str( $options_output_infos_selector ) != "1": + --output_archive $output_archive + #end if + --input_enzyme $options_enzyme.options_enzyme_selector + --enzyme1 $options_enzyme.enzyme + #if str( $options_enzyme.options_enzyme_selector ) == "2": + --enzyme2 $options_enzyme.enzyme2 + #end if + --outype $outype + --qualitenc $options_quality.qualitenc + #if $capture: + -D + #end if + --activate_advanced_options $activate_advanced_options + -t $options_advanced.truncate + #if $options_advanced.discard: + -q + #end if + #if $options_advanced.rescue: + -r + #end if + -w $options_advanced.sliding + -s $options_advanced.score + #if $options_advanced.remove: + -c + #end if + #if $options_advanced.inline: + --inline_null + #end if + #if $options_advanced.index: + --index_null + #end if + #if $options_advanced.inlinein: + --inline_inline + #end if + #if $options_advanced.indexind: + --index_index + #end if + #if $options_advanced.inlineind: + --inline_index + #end if + #if $options_advanced.indexin: + --index_inline + #end if + --logfile $output + +</command> + +<inputs> + + <conditional name="options_type"> + <param name="options_type_selector" type="select" label="Single-end or paired-end reads files"> + <option value="single" selected="True">Single-end files</option> + <option value="paired">Paired-end files</option> + </param> + <when value="single"> + <param name="inputs_single" format="fastq,fastq.gz" type="data" multiple="true" label="singles-end reads infile(s)" help="input files" /> + </when> + <when value="paired"> + <param name="inputs_paired1" format="fastq,fastq.gz" type="data" multiple="true" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" /> + <param name="inputs_paired2" format="fastq,fastq.gz" type="data" multiple="true" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" /> + </when> + </conditional> + <param name="inputype" type="select" format="text" label="Inputs format"> + <option value="fastq" selected="True">fastq</option> + <option value="gzfastq">fastq.gz</option> + <option value="bustard">Illumina BUSTARD</option> + </param> + <param name="barcode" type="data" format="tabular,txt" label="Barcode file" help="Barcode file" /> + + <param name="sample_name" type="text" value="sample" label="Sample name" help="Precise the sample name if using several NGS runs" /> + + <conditional name="options_enzyme"> + <param name="options_enzyme_selector" type="select" label="Number of enzymes"> + <option value="1" >One</option> + <option value="2">Two</option> + </param> + <when value="1"> + <param name="enzyme" type="select" format="text" label="Enzyme" help="provide the restriction enzyme used" > + <option value="apeKI">apeKI</option> + <option value="bamHI">bamHI</option> + <option value="claI">claI</option> + <option value="dpnII">dpnII</option> + <option value="eaeI">eaeI</option> + <option value="ecoRI">ecoRI</option> + <option value="ecoT22I">ecoT22I</option> + <option value="hindIII">hindIII</option> + <option value="mluCI">mluCI</option> + <option value="mseI">mseI</option> + <option value="mspI">mspI</option> + <option value="ndeI">ndeI</option> + <option value="nlaIII">nlaIII</option> + <option value="notI">notI</option> + <option value="nsiI">nsiI</option> + <option value="pstI">pstI</option> + <option value="sau3AI">sau3AI</option> + <option value="sbfI">sbfI</option> + <option value="sexAI">sexAI</option> + <option value="sgrAI">sgrAI</option> + <option value="sphI">sphI</option> + <option value="taqI">taqI</option> + <option value="xbaI">xbaI</option> + </param> + </when> + <when value="2"> + <param name="enzyme" type="select" format="text" label="Enzyme" help="provide the restriction enzyme used" > + <option value="apeKI">apeKI</option> + <option value="bamHI">bamHI</option> + <option value="claI">claI</option> + <option value="dpnII">dpnII</option> + <option value="eaeI">eaeI</option> + <option value="ecoRI">ecoRI</option> + <option value="ecoT22I">ecoT22I</option> + <option value="hindIII">hindIII</option> + <option value="mluCI">mluCI</option> + <option value="mseI">mseI</option> + <option value="mspI">mspI</option> + <option value="ndeI">ndeI</option> + <option value="nlaIII">nlaIII</option> + <option value="notI">notI</option> + <option value="nsiI">nsiI</option> + <option value="pstI">pstI</option> + <option value="sau3AI">sau3AI</option> + <option value="sbfI">sbfI</option> + <option value="sexAI">sexAI</option> + <option value="sgrAI">sgrAI</option> + <option value="sphI">sphI</option> + <option value="taqI">taqI</option> + <option value="xbaI">xbaI</option> + </param> + <param name="enzyme2" type="select" format="text" label="Second enzyme" help="provide the second restriction enzyme used" > + <option value="apeKI">apeKI</option> + <option value="bamHI">bamHI</option> + <option value="claI">claI</option> + <option value="dpnII">dpnII</option> + <option value="eaeI">eaeI</option> + <option value="ecoRI">ecoRI</option> + <option value="ecoT22I">ecoT22I</option> + <option value="hindIII">hindIII</option> + <option value="mluCI">mluCI</option> + <option value="mseI">mseI</option> + <option value="mspI">mspI</option> + <option value="ndeI">ndeI</option> + <option value="nlaIII">nlaIII</option> + <option value="notI">notI</option> + <option value="nsiI">nsiI</option> + <option value="pstI">pstI</option> + <option value="sau3AI">sau3AI</option> + <option value="sbfI">sbfI</option> + <option value="sexAI">sexAI</option> + <option value="sgrAI">sgrAI</option> + <option value="sphI">sphI</option> + <option value="taqI">taqI</option> + <option value="xbaI">xbaI</option> + </param> + </when> + </conditional> + <param name="capture" type="boolean" label="Capture discarded reads to a file" /> + <section name="options_quality" title="quality options" expanded="False"> + <param name="qualitenc" type="select" format="text" label="Quality encoded type" help="specify how quality scores are encoded, 'phred33' (Illumina 1.8+, Sanger, default) or 'phred64' (Illumina 1.3 - 1.5)" > + <option value="phred33">phred33</option> + <option value="phred64">phred64</option> + </param> + </section> + <param name="activate_advanced_options" type="boolean" label="Activate advanced options" help="advanced options are defined below" /> + <section name="options_advanced" title="advanced options" expanded="False"> + <param name="sliding" type="float" value="0.15" label="set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15)" /> + <param name="score" type="integer" value="10" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" /> + <param name="remove" type="boolean" checked="false" default="false" label="Clean data, remove any read with an uncalled base" /> + <param name="discard" type="boolean" checked="false" default="false" label="Discard reads with low quality scores"/> + <param name="rescue" type="boolean" checked="false" default="false" label="Rescue barcodes and RAD-Tags?"/> + <param name="truncate" type="integer" value="-1" label="Truncate final read length to this value" help="default = -1" /> + <param name="inline" type="boolean" checked="true" default="true" label="Barcode options -> inline_null" help="barcode is inline with sequence, occurs only on single-end read" /> + <param name="index" type="boolean" checked="false" default="false" label="Barcode options -> index_null" help="barcode is provided in FASTQ header, occurs only on single-end read"/> + <param name="inlinein" type="boolean" checked="false" default="false" label="Barcode options -> inline_inline" help="barcode is inline with sequence, occurs on single and paired-end read" /> + <param name="indexind" type="boolean" checked="false" default="false" label="Barcode options -> index_index" help="barcode is provided in FASTQ header, occurs on single and paired-end read" /> + <param name="inlineind" type="boolean" checked="false" default="false" label="Barcode options -> inline_index" help="barcode is inline with sequence on single-end read, occurs in FASTQ header for paired-end read" /> + <param name="indexin" type="boolean" checked="false" default="false" label="Barcode options -> index_inline" help="barcode occurs in FASTQ header for single-end read, is inline with sequence on paired-end read" /> + </section> + <param name="outype" type="select" format="text" label="Output format" help="output type, either 'fastq' or 'fasta' (default fastq)" > + <option value="fastq">fastq</option> + <option value="fasta">fasta</option> + </param> + + <param name="options_output_infos_selector" type="select" label="Output type"> + <option value="1">Normal (a fastq file by barcode)</option> + <option value="2" selected="True">Additional zip archive with all files (Normal + one archive with all fastq files)</option> + <option value="3">Only a zip archive with all files (one archive with all fastq files)</option> + </param> + +</inputs> +<outputs> + + <data format="txt" name="output" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" /> + <data format="txt" name="additional" label="fast(a/q) file with ${tool.name}" hidden="true"> + <discover_datasets pattern="__designation_and_ext__" directory="galaxy_outputs" visible="true" /> + </data> + <data format="zip" name="output_archive" label="all_files.zip with ${tool.name} on ${on_string}: demultiplexed and cleaned reads "> + <filter>options_output_infos_selector != "1"</filter> + </data> + <data format="fastq" name="discard_file" label="discard.fastq with ${tool.name} on ${on_string}: demultiplexed and cleaned reads "> + <filter>capture</filter> + </data> + + +</outputs> + +<stdio> + <exit_code range="1" level="fatal" description="Error in Stacks Process radtag execution" /> +</stdio> + + +<help> + +.. class:: infomark + +**What it does** + +This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are +errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the +average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some +seqeuncing errors while elimating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but can be +specified on the command line (the threshold and window size can be adjusted). +The process_radtags program can: +handle data that is barcoded, either inline or using an index, or unbarcoded. +use combinatorial barcodes. +check and correct for a restriction enzyme cutsite for single or double-digested +data. +filter adapter sequence while allowing for sequencing error in the adapter pattern. +process individual files or whole directories of files. +directly read gzipped data +filter reads based on Illumina's Chastity filter + +-------- + +**Help** + +Input files: + +- FASTQ, FASTA, zip, tar.gz + +- Barcode File Format + +The barcode file is a very simple format : one barcode per line. + + CGATA + CGGCG + GAAGC + GAGAT + CGATA + CGGCG + GAAGC + GAGAT + +Combinatorial barcodes are specified, one per column, separated by a tab:: + + CGATA ACGTA + CGGCG CGTA + GAAGC CGTA + GAGAT CGTA + CGATA AGCA + CGGCG AGCA + GAAGC AGCA + GAGAT AGCA + + +Instructions to add the functionality of archives management in Galaxy on the `eBiogenouest HUB wiki <https://www.e-biogenouest.org/wiki/ManArchiveGalaxy>`_ . + +-------- + + +**Created by:** + +Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko + +-------- + +**Project links:** + +`STACKS website <http://creskolab.uoregon.edu/stacks/>`_ . + +`STACKS manual <http://creskolab.uoregon.edu/stacks/stacks_manual.pdf>`_ . + +`STACKS google group <https://groups.google.com/forum/#!forum/stacks-users>`_ . + +-------- + +**References:** + +-J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013. + +-J. Catchen, S. Bassham, T. Wilson, M. Currey, C. O'Brien, Q. Yeates, and W. Cresko. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Molecular Ecology. 2013. + +-J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1:171-182, 2011. + +-A. Amores, J. Catchen, A. Ferrara, Q. Fontenot and J. Postlethwait. Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication. Genetics, 188:799'808, 2011. + +-P. Hohenlohe, S. Amish, J. Catchen, F. Allendorf, G. Luikart. RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow trout and westslope cutthroat trout. Molecular Ecology Resources, 11(s1):117-122, 2011. + +-K. Emerson, C. Merz, J. Catchen, P. Hohenlohe, W. Cresko, W. Bradshaw, C. Holzapfel. Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Science, 107(37):16196-200, 2010. + +-------- + +**Integrated by:** + +Yvan Le Bras and Cyril Monjeaud + +GenOuest Bio-informatics Core Facility + +UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France) + +support@genouest.org + +If you use this tool in Galaxy, please cite : + +`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. <https://www.e-biogenouest.org/resources/128>`_ + + + +</help> +<citations> + <citation type="doi">10.1111/mec.12354</citation> + <citation type="doi">10.1111/mec.12330</citation> + <citation type="doi">10.1534/g3.111.000240</citation> + <citation type="doi">10.1534/genetics.111.127324</citation> + <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation> + <citation type="doi">10.1073/pnas.1006538107</citation> + + <citation type="bibtex">@INPROCEEDINGS{JOBIM2013, + author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.}, + title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France}, + booktitle = {JOBIM 2013 Proceedings}, + year = {2013}, + url = {https://www.e-biogenouest.org/resources/128}, + pages = {97-106} + }</citation> +</citations> +</tool> +