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date | Tue, 17 Jul 2018 11:48:59 -0400 |
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<tool id="ctat_rsem_align_and_estimate_abundance" name="ctat_rsem_align_and_estimate_abundance" version="1.0.0" profile="17.05"> <description>run RSEM to estimate transcript abundances</description> <requirements> <requirement type="package" version="2.7">python</requirement> <requirement type="package">subprocess32</requirement> <requirement type="package">bzip2</requirement> <requirement type="package" version="1.3.0">rsem</requirement> <requirement type="package" version="3">bioconductor-edger</requirement> <requirement type="package" version="2">bioconductor-qvalue</requirement> <requirement type="package" version="2.6.6">trinity</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ python $__tool_directory__/ctat_trinity_tool_wrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie2 --trinity_mode --prep_reference --output_dir "subdir" ## Inputs. #if str($inputs.paired_or_single) == "paired": --left $inputs.left_input --right $inputs.right_input #if $inputs.left_input.ext == 'fa': --seqType fa #else: --seqType fq #end if #if str($inputs.library_type) != "None": --SS_lib_type $inputs.library_type #end if #else: --single $inputs.input #if str($inputs.input.ext) == 'fa': --seqType fa #else: --seqType fq #end if #if str($inputs.library_type) != "None": --SS_lib_type $inputs.library_type #end if #end if ]]> </command> <inputs> <param format="fasta" name="transcripts" type="data" label="Transcripts Fasta" help="Fasta sequences against which reads are aligned. This may be the Assembled Transcripts file from Trinity." /> <conditional name="inputs"> <param name="paired_or_single" type="select" label="Paired or Single-end data?"> <option value="paired">Paired</option> <option value="single">Single</option> </param> <when value="paired"> <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> <param name="library_type" type="select" label="Strand-specific Library Type"> <option value="None">None</option> <option value="FR">FR</option> <option value="RF">RF</option> </param> </when> <when value="single"> <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> <param name="library_type" type="select" label="Strand-specific Library Type"> <option value="None">None</option> <option value="F">F</option> <option value="R">R</option> </param> </when> </conditional> </inputs> <outputs> <data format="txt" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="subdir/RSEM.isoforms.results"/> <data format="txt" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="subdir/RSEM.genes.results"/> </outputs> <tests> <test> <param name="transcripts" value="reads.simPE.Trinity.fasta" /> <param name="paired_or_single" value="paired" /> <param name="left_input" value="reads.left.simPE.fq" /> <param name="right_input" value="reads.right.simPE.fq" /> <param name="library_type" value="None" /> <output name="transcript_counts" > <assert_contents> <has_line_matching expression=".+" /> <has_line line="transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct" /> </assert_contents> </output> <output name="gene_counts" > <assert_contents> <has_line_matching expression=".+" /> <has_line line="gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM" /> </assert_contents> </output> </test> <test> <param name="transcripts" value="Sp.Trinity.fasta" /> <param name="paired_or_single" value="paired" /> <param name="left_input" value="Sp_ds.left.fq" /> <param name="right_input" value="Sp_ds.right.fq" /> <param name="library_type" value="None" /> <output name="transcript_counts" > <assert_contents> <has_line_matching expression=".+" /> <has_line line="transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct" /> </assert_contents> </output> <output name="gene_counts" > <assert_contents> <has_line_matching expression=".+" /> <has_line line="gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM" /> </assert_contents> </output> </test> <test> <param name="transcripts" value="Sp.Trinity.fasta" /> <param name="paired_or_single" value="paired" /> <param name="left_input" value="Sp_hs.left.fq" /> <param name="right_input" value="Sp_hs.right.fq" /> <param name="library_type" value="None" /> <output name="transcript_counts" > <assert_contents> <has_line_matching expression=".+" /> <has_line line="transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct" /> </assert_contents> </output> <output name="gene_counts" > <assert_contents> <has_line_matching expression=".+" /> <has_line line="gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM" /> </assert_contents> </output> </test> </tests> <help> .. class:: infomark Use RSEM to generate transcript quantification for genes and isoforms. To learn more about RSEM read their paper_ or visit their website_. If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols publication_ . .. _paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323 .. _publication: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html .. _website: http://deweylab.biostat.wisc.edu/rsem/README.html .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki </help> <citations> <citation type="doi">10.1038/nbt.1883</citation> </citations> </tool>