Mercurial > repos > artbio > trinity
diff trinity.xml @ 0:b3fe7c4ca5aa draft default tip
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
| author | artbio |
|---|---|
| date | Sat, 17 Mar 2018 17:43:58 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinity.xml Sat Mar 17 17:43:58 2018 -0400 @@ -0,0 +1,295 @@ +<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.3"> + <description>de novo assembly of RNA-Seq data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + if [ -z "\$GALAXY_MEMORY_MB" ] ; then + GALAXY_MEMORY_GB=1 ; + else + GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ; + fi ; + + if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then + workdir=`pwd` ; + cd "\$TRINITY_SCRATCH_DIR" ; + fi ; + + #if $additional_params.guided.is_guided == "yes": + ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' && + ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' && + #end if + Trinity --no_version_check + + ## Inputs + #if $pool.pool_mode == "Yes": + #if str($pool.inputs.paired_or_single) == "single": + --single ${ ','.join(['"%s"' % x for x in $pool.inputs.input]) } + #if $pool.inputs.input[0].is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + + #if $pool.inputs.strand.is_strand_specific: + --SS_lib_type $pool.inputs.strand.library_type + #end if + #elif str($pool.inputs.paired_or_single) == "paired": + --left ${ ','.join(['"%s"' % x for x in $pool.inputs.left_input]) } + + --right ${ ','.join(['"%s"' % x for x in $pool.inputs.right_input]) } + + #if $pool.inputs.left_input[0].is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + @COMMAND_PAIRED_STRAND_JACCARD@ + #elif str($pool.inputs.paired_or_single) == "paired_collection": + --left ${ ','.join(['"%s"' % x.forward for x in $pool.inputs.pair_input]) } + --right ${ ','.join(['"%s"' % x.reverse for x in $pool.inputs.pair_input]) } + #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + @COMMAND_PAIRED_STRAND_JACCARD@ + #end if + #elif $pool.pool_mode == "No": + #if $pool.inputs.paired_or_single == "unmerged_paired_collection": + --left $pool.inputs.pair_input.forward + + --right $pool.inputs.pair_input.reverse + + #if $pool.inputs.pair_input.forward.is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + @COMMAND_PAIRED_STRAND_JACCARD@ + #elif $pool.inputs.paired_or_single == "unmerged_single_collection": + --single $pool.inputs.input + + #if $pool.inputs.input.is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + + #if $pool.inputs.strand.is_strand_specific: + --SS_lib_type $pool.inputs.strand.library_type + #end if + #end if + #end if + $norm + + ## Additional parameters. + #if $additional_params.min_contig_length: + --min_contig_length $additional_params.min_contig_length + #end if + #if $additional_params.long_reads: + --long_reads $additional_params.long_reads + #end if + #if $additional_params.guided.is_guided == "yes": + --genome_guided_bam 'localbam.bam' + + #if $additional_params.guided.genome_guided_min_coverage: + --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage + #end if + + #if $additional_params.guided.genome_guided_min_reads_per_partition: + --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition + #end if + + #if $additional_params.guided.genome_guided_max_intron: + --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron + #end if + #end if + + #if $additional_params.min_kmer_cov: + --min_kmer_cov $additional_params.min_kmer_cov + #end if + + ## CPU and butterfly options. + --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr' + + ## > $trinity_log 2>&1 + + && + + if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then + mkdir -p "\$workdir/trinity_out_dir"; + cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir"; + cd "\$workdir"; + fi ; + + ]]></command> + <inputs> + <conditional name="pool"> + <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" > + <option value="No">No</option> + <option value="Yes" selected="True">Yes</option> + </param> + <when value="Yes" > + <conditional name="inputs"> + <param name="paired_or_single" type="select" label="Paired or Single-end data?"> + <option value="single" selected="true">Single-end</option> + <option value="paired">Paired-end</option> + <option value="paired_collection">Paired-end collection</option> + </param> + <when value="single"> + <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/> + <conditional name="strand"> + <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> + <when value="false"> + </when> + <when value="true"> + <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> + <option value="F">F</option> + <option value="R">R</option> + </param> + </when> + </conditional> + </when> + <when value="paired"> + <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" /> + <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" /> + <expand macro="input_paired_strand_jaccard" /> + </when> + <when value="paired_collection"> + <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/> + <expand macro="input_paired_strand_jaccard" /> + </when> + </conditional> + </when> + <when value="No"> + <conditional name="inputs"> + <param name="paired_or_single" type="select" label="Paired or Single-end data?"> + <option value="unmerged_single_collection">Single-end</option> + <option value="unmerged_paired_collection">Paired-end</option> + </param> + <when value="unmerged_single_collection"> + <param name="input" argument="--single" type="data" format="fasta,fastqsanger" label="Single-end reads" help="Elements of collection will NOT be merged"/> + <conditional name="strand"> + <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> + <when value="false"> + </when> + <when value="true"> + <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> + <option value="F">F</option> + <option value="R">R</option> + </param> + </when> + </conditional> + </when> + <when value="unmerged_paired_collection"> + <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/> + <expand macro="input_paired_strand_jaccard" /> + </when> + </conditional> + </when> + </conditional> + <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/> + <section name="additional_params" title="Additional Options" expanded="False"> + <param name="min_contig_length" argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/> + + <conditional name="guided"> + <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" /> + <param name="genome_guided_max_intron" argument="--genome_guided_max_intron" type="integer" value="" min="1" label="Maximum allowed intron length (also maximum fragment span on genome)"/> + <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/> + <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/> + </when> + </conditional> + + <param name="long_reads" argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/> + + <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/> + </section> + </inputs> + <outputs> + <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> + </outputs> + <tests> + <test> + <param name="pool_mode" value="No" /> + <param name="paired_or_single" value="unmerged_paired_collection"/> + <param name="pair_input"> + <collection type="paired"> + <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> + <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> + </collection> + </param> + <param name="is_strand_specific" value="true"/> + <param name="norm" value="true"/> + <param name="library_type" value="RF"/> + <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" /> + </test> + <test> + <param name="pool_mode" value="No" /> + <param name="paired_or_single" value="unmerged_single_collection"/> + <param name="input" value="reads.left.fq" ftype="fastqsanger"/> + <param name="is_strand_specific" value="true"/> + <param name="norm" value="false"/> + <param name="library_type" value="F"/> + <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" /> + </test> + <test> + <param name="pool_mode" value="Yes" /> + <param name="paired_or_single" value="paired"/> + <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> + <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> + <param name="is_strand_specific" value="true"/> + <param name="norm" value="false"/> + <param name="library_type" value="RF"/> + <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" /> + </test> + <test> + <param name="pool_mode" value="Yes" /> + <param name="paired_or_single" value="paired"/> + <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> + <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> + <param name="is_strand_specific" value="true"/> + <param name="norm" value="true"/> + <param name="library_type" value="RF"/> + <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> + </test> + <test> + <param name="pool_mode" value="Yes" /> + <param name="paired_or_single" value="paired_collection"/> + <param name="pair_input"> + <collection type="list:paired"> + <element name="pair1"> + <collection type="paired"> + <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> + <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> + </collection> + </element> + <element name="pair2"> + <collection type="paired"> + <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> + <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> + </collection> + </element> + </collection> + </param> + <param name="is_strand_specific" value="true"/> + <param name="norm" value="true"/> + <param name="library_type" value="RF"/> + <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> + </test> + </tests> + <help> +Trinity_ assembles transcript sequences from Illumina RNA-Seq data. + +.. _Trinity: http://trinityrnaseq.github.io + </help> + <expand macro="citation" /> +</tool>