Mercurial > repos > peterjc > clc_assembly_cell
view tools/clc_assembly_cell/clc_mapper.xml @ 0:0996169ac2e8 draft
Uploaded v0.0.2, previously only on the TestToolShed
| author | peterjc |
|---|---|
| date | Fri, 21 Nov 2014 06:41:12 -0500 |
| parents | |
| children | 5ae1c0312aaa |
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<tool id="clc_mapper" name="CLC Mapper" version="0.0.2"> <description>Maps reads giving a SAM/BAM file</description> <requirements> <requirement type="binary">clc_mapper</requirement> <requirement type="binary">clc_cas_to_sam</requirement> <requirement type="binary">samtools</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command> <command>echo Mapping reads with clc_mapper... && \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper #for $ref in $references #if str($ref.ref_type)=="circular" -d -z "$ref.ref_file" #else -d "$ref.ref_file" #end if #end for #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 -o "temp_job.cas" --cpus \${GALAXY_SLOTS:-4} ## TODO - filtering out the progress lines seems to mess up the multiple commands ## | grep -v "^Progress: " ##=========================================== ## TODO - I've required all the input in Sanger FASTQ format (or FASTA) so can ## use the offset 33, rather then the CLCbio default of 64 which is only for ## obsolete Illumina FASTQ files. Really need this option per input file... && echo Converting CAS file to BAM with clc_cas_to_sam... && /mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_cas_to_sam --cas "temp_job.cas" -o "temp_job.bam" --no-progress --qualityoffset 33 && rm "temp_job.cas" ##=========================================== && echo Sorting BAM file with samtools... && samtools sort "temp_job.bam" "temp_sorted" && mv "temp_sorted.bam" "$out_bam" && echo Indexing BAM file with samtools... && samtools index "$out_bam"</command> <stdio> <!-- Assume anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> <!-- Job splitting with merge via clc_join_mappings? --> <inputs> <!-- Support linear and circular references (-z) --> <repeat name="references" title="Reference Sequence" min="1"> <param name="ref_file" type="data" format="fasta" required="true" label="Reference sequence(s) (FASTA)" /> <param name="ref_type" type="select" label="Reference type"> <option value="linear">Linear (e.g. most chromosomes)</option> <option value="circular">Circular (e.g. bacterial chromosomes, mitochondria)</option> </param> </repeat> <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="fastqsanger,fasta" required="true" label="Read file one" help="FASTA or Sanger FASTQ accepted." /> <param name="filename2" type="data" format="fastqsanger,fasta" required="true" label="Read file two" help="FASTA or Sanger FASTQ accepted." /> </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="fastqsanger,fasta" required="true" label="Interleaved read file" help="FASTA or Sanger FASTQ accepted."/> </when> <when value="none"> <param name="filenames" type="data" format="fastqsanger,fasta" multiple="true" required="true" label="Read file(s)" help="Multiple files allowed, for example several files of orphan reads. FASTA or Sanger FASTQ accepted." /> </when> </conditional> </repeat> <!-- Length fraction (-l), default 0.5 --> <!-- Similarity (-s), default 0.8 --> <!-- Option for unmapped reads via clc_unmapped_reads ? --> </inputs> <outputs> <data name="out_bam" format="bam" label="CLCbio mapping (BAM)" /> </outputs> <tests> <!-- CLC's SAM header @PG and @RG lines include filenames so will change --> <test> <param name="ref_file" value="NC_010642.fna" ftype="fasta" /> <param name="ref_type" value="circular" /> <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" /> <output name="out_fasta" file="SRR639755_mito_pairs_vs_NC_010642_clc.bam" ftype="bam" lines_diff="4"/> </test> </tests> <help> **What it does** Runs the CLCbio tool ``clc_mapper`` which produces a proprietary binary CAS format file, which is immediately processed using ``clc_cas_to_sam`` to generate a self-contained standard BAM file, which is then sorted and indexed using ``samtools``. **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>