Mercurial > repos > peterjc > clc_assembly_cell
view tools/clc_assembly_cell/clc_assembler.xml @ 3:9fe1a922353b draft
v0.0.5 option to discard unmapped read; env var bugfix
author | peterjc |
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date | Wed, 11 May 2016 06:49:58 -0400 |
parents | 139b6f0a0bb5 |
children | 46a667b5e19e |
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<tool id="clc_assembler" name="CLC assembler" version="0.0.4"> <description>Assembles reads giving a FASTA file</description> <requirements> <requirement type="binary">clc_assembler</requirement> </requirements> <stdio> <!-- Assume anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> <version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command> <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler #for $rg in $read_group ##-------------------------------------- #if str($rg.segments.type) == "paired" -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2" #end if ##-------------------------------------- #if str($rg.segments.type) == "interleaved" -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q "$rg.segments.filename" #end if ##-------------------------------------- #if str($rg.segments.type) == "none" -p no -q #for $f in $rg.segments.filenames "$f" #end for #end if ##-------------------------------------- #end for -m $min_contig_len -o "$out_fasta" --cpus \${GALAXY_SLOTS:-4} -v | grep -v "^Progress: "</command> <inputs> <repeat name="read_group" title="Read Group" min="1"> <conditional name="segments"> <param name="type" type="select" label="Are these paired reads?"> <option value="paired">Paired reads (as two files)</option> <option value="interleaved">Paired reads (as one interleaved file)</option> <option value="none">Unpaired reads (single or orphan reads)</option> </param> <when value="paired"> <param name="placement" type="select" label="Pairing type (segment placing)"> <option value="fb">---> <--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option> <option value="bf"><--- ---> (e.g. Solexa/Illumina mate-pair library)</option> <option value="ff">---> ---></option> <option value="bb"><--- <---</option> </param> <param name="dist_mode" type="select" label="How is the fragment distance measured?"> <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option> <option value="se">Start to end</option> <option value="es">End to start</option> <option value="ee">End to end</option> </param> <!-- TODO - min/max validation done via the <code> tag? --> <param name="min_size" type="integer" optional="false" min="0" value="" label="Minimum size of 'good' DNA templates in the library preparation" /> <param name="max_size" type="integer" optional="false" min="0" value="" label="Maximum size of 'good' DNA templates in the library preparation" /> <param name="filename1" type="data" format="fastq,fasta" required="true" label="Read file one"/> <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/> </when> <when value="interleaved"> <param name="placement" type="select" label="Pairing type (segment placing)"> <option value="fb">---> <--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option> <option value="bf"><--- ---> (e.g. Solexa/Illumina mate-pair library)</option> <option value="ff">---> ---></option> <option value="bb"><-- <--</option> </param> <param name="dist_mode" type="select" label="How is the fragment distance measured?"> <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option> <option value="se">Start to end</option> <option value="es">End to start</option> <option value="ee">End to end</option> </param> <!-- TODO - min/max validation done via the <code> tag? --> <param name="min_size" type="integer" optional="false" min="0" value="" label="Minimum size of 'good' DNA templates in the library preparation" /> <param name="max_size" type="integer" optional="false" min="0" value="" label="Maximum size of 'good' DNA templates in the library preparation" /> <param name="filename" type="data" format="fastq,fasta" required="true" label="Interleaved read file"/> </when> <when value="none"> <param name="filenames" type="data" format="fastq,fasta" multiple="true" required="true" label="Read file(s)" help="Multiple files allowed, for example several files of orphan reads." /> </when> </conditional> </repeat> <param name="min_contig_len" type="integer" optional="false" min="1" value="200" label="Minimum contig length"/> <!-- Word size? --> <!-- Bubble size? --> <!-- Scaffolding options? --> <!-- AGP / GFF output? --> </inputs> <!-- min/max validation? <code file="clc_validator.py" /> --> <outputs> <data name="out_fasta" format="fasta" label="CLCbio assember contigs (FASTA)" /> </outputs> <tests> <test> <param name="read_group_0|segments|type" value="interleaved" /> <param name="read_group_0|segments|placement" value="fb" /> <param name="read_group_0|segments|dist_mode" value="ss" /> <param name="read_group_0|segments|min_size" value="1" /> <param name="read_group_0|segments|max_size" value="1000" /> <param name="read_group_0|segments|dist_mode" value="ss" /> <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="min_contig_len" value="200" /> <output name="out_fasta" file="SRR639755_mito_pairs.clc4_de_novo.fasta" ftype="fasta" /> </test> </tests> <help> **What it does** Runs the ``clc_assembler`` tool giving a FASTA output file. You would then typically map the same set of reads onto this assembly using ``cls_mapper`` to any perform downstream analysis using the mapped reads. **Citation** If you use this Galaxy tool in work leading to a scientific publication please cite this wrapper as: Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell CLC Assembly Cell, CLC bio (2008--2015) http://www.clcbio.com/products/clc-assembly-cell/ This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell </help> <citations> <citation type="bibtex"> @MISC{clcbio, AUTHOR = {CLC Bio} title ={{CLC Assembly Cell}}, url = {http://www.clcbio.com/products/clc-assembly-cell/}, year = {2008--2015} } </citation> </citations> </tool>