Mercurial > repos > peterjc > clc_assembly_cell
diff tools/clc_assembly_cell/clc_assembler.xml @ 0:0996169ac2e8 draft
Uploaded v0.0.2, previously only on the TestToolShed
author | peterjc |
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date | Fri, 21 Nov 2014 06:41:12 -0500 |
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children | 5ae1c0312aaa |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/clc_assembly_cell/clc_assembler.xml Fri Nov 21 06:41:12 2014 -0500 @@ -0,0 +1,133 @@ +<tool id="clc_assembler" name="CLC assembler" version="0.0.2"> + <description>Assembles reads giving a FASTA file</description> + <requirements> + <requirement type="binary">clc_assembler</requirement> + </requirements> + <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> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <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 + +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> +</tool>