Mercurial > repos > trinity_ctat > align_and_estimate_abundance
diff align_and_estimate_abundance.xml @ 0:a9723c18d389 draft
Adding align_and_estimate_abundance tool.
| author | trinity_ctat |
|---|---|
| date | Thu, 21 Sep 2017 15:11:18 -0400 |
| parents | |
| children | 78d12a725443 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align_and_estimate_abundance.xml Thu Sep 21 15:11:18 2017 -0400 @@ -0,0 +1,160 @@ +<tool id="RSEM_abundance_estimation" name="align_and_estimate_abundance" version="2.0.0"> + + <description>run RSEM to estimate transcript abundances</description> + + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="2.4.0">trinity</requirement> + </requirements> + + <command interpreter="python"> + <![CDATA[ + trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir "subdir" + + ## Inputs. + #if str($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 $inputs.library_type + #end if + #end if + ]]> + + </command> + <inputs> + <param format="fasta" name="transcripts" type="data" label="Transcripts Fasta" help="Fasta sequences against which reads are aligned. This may be the Assembled Transcripts file from Trinity." /> + + <conditional name="inputs"> + <param name="paired_or_single" type="select" label="Paired or Single-end data?"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + <when value="paired"> + <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> + <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="None">None</option> + <option value="FR">FR</option> + <option value="RF">RF</option> + </param> + + </when> + <when value="single"> + <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="None">None</option> + <option value="F">F</option> + <option value="R">R</option> + </param> + + </when> + </conditional> + </inputs> + + <outputs> + <data format="text" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="subdir/RSEM.isoforms.results"/> + <data format="text" name="gene_counts" label="${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>