Mercurial > repos > iuc > optitype
diff optitype.xml @ 0:fd974c5df8bc draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
| author | iuc |
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| date | Wed, 17 Feb 2021 08:10:24 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/optitype.xml Wed Feb 17 08:10:24 2021 +0000 @@ -0,0 +1,213 @@ +<tool id="optitype" name="OptiType" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>HLA genotyping predictions from NGS data</description> + <macros> + <token name="@TOOL_VERSION@">1.3.5</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">optitype</requirement> + </requirements> + <command detect_errors="aggressive"> +<![CDATA[ +export MPLCONFIGDIR=\$TEMP && +#set $fastqs = [] +#if str( $fastq_input.fastq_input_selector ) == "paired": + ln -s '${fastq_input.fastq_input1}' reads_1.fastq + && ln -s '${fastq_input.fastq_input2}' reads_2.fastq + #set $fastqs = ['reads_1.fastq','reads_2.fastq'] +#elif str( $fastq_input.fastq_input_selector ) == "paired_collection": + ln -s '${fastq_input.fastq_input1.forward}' reads_1.fastq + && ln -s '${fastq_input.fastq_input1.reverse}' reads_2.fastq + #set $fastqs = ['reads_1.fastq','reads_2.fastq'] +#elif str( $fastq_input.fastq_input_selector ) == "single": + ln -s '${fastq_input.fastq_input1}' reads.fastq + #set $fastqs = ['reads.fastq'] +#end if +&& RAZERS3=`which razers3` +&& sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\${GALAXY_SLOTS}/" > config.ini +#set $input_fq = ' '.join($fastqs) +&& OptiTypePipeline.py +$read_type --input ${' '.join($fastqs)} +#if str($beta) != '': + --beta $beta +#end if +#if str($enumerations) != '': + --enumerate $enumerations +#end if +--config "`pwd`/config.ini" +--outdir outdir +&& cp outdir/*/*_coverage_plot.pdf '$coverage_plot' +&& cp outdir/*/*_result.tsv '$result' +]]> + </command> + <configfiles> + <configfile name="optitype_config"><![CDATA[ +[mapping] + +# Absolute path to RazerS3 binary, and number of threads to use for mapping + +razers3=path_to_razers3 +threads=16 + +[ilp] + +# A Pyomo-supported ILP solver. The solver must be globally accessible in the +# environment OptiType is run, so make sure to include it in PATH. +# Note: this is NOT a path to the solver binary, but a keyword argument for +# Pyomo. Examples: glpk, cplex, cbc. + +solver=$solver +threads=1 + +[behavior] + +# tempdir=/path/to/tempdir # we may enable this setting later. Not used now. + +# Delete intermediate bam files produced by RazerS3 after OptiType finished +# loading them. If you plan to re-analyze your samples with different settings +# disabling this option can be a time-saver, as you'll be able to pass the bam +# files to OptiType directly as input and spare the expensive read mapping +# step. + +deletebam=true + +# In paired-end mode one might want to use reads with just one mapped end (e.g., +# the other end falls outside the reference region). This setting allows the +# user to keep them with an optionally reduced weight. A value of 0 means they +# are discarded for typing, 0.2 means single reads are "worth" 20% of paired +# reads, and a value of 1 means they are treated as valuable as properly mapped +# read pairs. Note: unpaired reads will be reported on the result coverage plots +# for completeness, regardless of this setting. + +unpaired_weight=$unpaired_weight + +# We call a read pair discordant if its two ends best-map to two disjoint sets +# of alleles. Such reads can be either omitted or either of their ends treated +# as unpaired hits. Note: discordant read pairs are reported on the coverage +# plots as unpaired reads, regardless of this setting. + +use_discordant=$use_discordant + ]]></configfile> + </configfiles> + <inputs> + <conditional name="fastq_input"> + <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> + <option value="paired">Paired</option> + <option value="single">Single</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="paired"> + <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="single"> + <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/> + </when> + <when value="paired_collection"> + <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> + </when> + </conditional> + <param name="read_type" type="select" label="Nucleotide Type" help=""> + <option value="--rna">RNA</option> + <option value="--dna">DNA</option> + </param> + <param name="beta" type="float" value="" min="0.0" max="0.1" optional="true" label="homozygosity beta" help="The beta value for for homozygosity detection (Leave blank for default: 0.009)"/> + <param name="enumerations" type="integer" value="" min="1" max="5" optional="true" label="Enumerations" help="The number of enumerations (Leave blank for default: 1)"/> + <param name="solver" type="select" label="ILP solver" help=""> + <option value="glpk">glpk</option> + <!-- Not currently in OptiType conda package + <option value="cbc">cbc</option> + <option value="cplex">cplex</option> + --> + </param> + <param name="unpaired_weight" type="float" value="0" min="0.0" max="1.0" label="unpaired_weight"> + <help><![CDATA[ +In paired-end mode one might want to use reads with just one mapped end (e.g., +the other end falls outside the reference region). This setting allows the +user to keep them with an optionally reduced weight. A value of 0 means they +are discarded for typing, 0.2 means single reads are "worth" 20% of paired +reads, and a value of 1 means they are treated as valuable as properly mapped +read pairs. Note: unpaired reads will be reported on the result coverage plots +for completeness, regardless of this setting. ]]> + </help> + </param> + <param name="use_discordant" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use_discordant"> + <help><![CDATA[ +We call a read pair discordant if its two ends best-map to two disjoint sets +of alleles. Such reads can be either omitted or either of their ends treated +as unpaired hits. Note: discordant read pairs are reported on the coverage +plots as unpaired reads, regardless of this setting. ]]> + </help> + </param> + </inputs> + <outputs> + <data name="coverage_plot" format="pdf" label="${tool.name} on ${on_string} coverage_plot.pdf"/> + <data name="result" format="tabular" label="${tool.name} on ${on_string} result.tsv"> + <actions> + <action name="column_names" type="metadata" default="Solution,A1,A2,B1,B2,C1,C2,Reads,Objective"/> + </actions> + </data> + </outputs> + <tests> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="rna/CRC_81_N_1_fished.fastq"/> + <param name="fastq_input2" ftype="fastqsanger" value="rna/CRC_81_N_2_fished.fastq"/> + </conditional> + <param name="read_type" value="--rna"/> + <param name="solver" value="glpk"/> + <output name="result"> + <assert_contents> + <has_text_matching expression="0\tA\*31:01\tA\*68:01\tB\*40:01\tB\*51:01\tC\*03:04\tC\*15:02\t13\d+.\d+\t12\d+.\d+"/> + </assert_contents> + </output> + </test> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="exome/NA11995_SRR766010_1_fished.fastq"/> + <param name="fastq_input2" ftype="fastqsanger" value="exome/NA11995_SRR766010_2_fished.fastq"/> + </conditional> + <param name="read_type" value="--dna"/> + <param name="solver" value="glpk"/> + <param name="enumerations" value="2"/> + <param name="unpaired_weight" value="0.2"/> + <output name="result"> + <assert_contents> + <has_text_matching expression="0\tA\*01:01\tA\*01:01\tB\*08:01\tB\*57:01\tC\*06:02\tC\*07:01\t3\d+.\d+\t3\d+.\d+"/> + <has_text_matching expression="1\tA\*01:01\tA\*01:01\tB\*08:01\tB\*08:01\tC\*06:02\tC\*07:01\t3\d+.\d+\t3\d+.\d+"/> + </assert_contents> + </output> + </test> + </tests> + <help> +<![CDATA[ +**OptiType** +============ + +OptiType_ is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. + +**INPUTS** + + RNA or DNA sequences in fastq format. + +**OUTPUTS** + + result.tsv A TAB-separated file of HLA genotyping predictions: + + :: + + A1 A2 B1 B2 C1 C2 Reads Objective + 0 A*31:01 A*68:01 B*40:01 B*51:01 C*15:02 C*03:04 132 128.43599999999998 + + + coverage_plot.pdf Plots of coverage of HLA genotyping predictions + +.. _OptiType: https://github.com/FRED-2/OptiType +]]> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu548</citation> + </citations> +</tool>