Mercurial > repos > iuc > trinity_align_and_estimate_abundance
diff align_and_estimate_abundance.xml @ 0:a21e229da9a1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
| author | iuc |
|---|---|
| date | Mon, 01 Aug 2016 14:43:15 -0400 |
| parents | |
| children | a966877db15b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align_and_estimate_abundance.xml Mon Aug 01 14:43:15 2016 -0400 @@ -0,0 +1,309 @@ +<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.0"> + <description>on a de novo assembly of RNA-Seq data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="1.1.2">bowtie</requirement> + <requirement type="package" version="2.2.6">bowtie2</requirement> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.2.28">rsem</requirement> + <requirement type="package" version="1.5.1">eXpress</requirement> + <requirement type="package" version="0.6.0">salmon</requirement> + </expand> + <expand macro="stdio"/> + <command><![CDATA[ + ln -s '$transcripts' input.fa && + + #if $inputs.paired_or_single == "paired": + #if $inputs.left_input.is_of_type('fasta'): + ln -s '$inputs.left_input' paired_left.fa && + ln -s '$inputs.right_input' paired_right.fa + #else: + ln -s '$inputs.left_input' paired_left.fq && + ln -s '$inputs.right_input' paired_right.fq + #end if + #else: + #if $inputs.left_input.is_of_type('fasta'): + ln -s '$inputs.input' single.fa + #else: + ln -s '$inputs.input' single.fq + #end if + #end if + + && + + align_and_estimate_abundance.pl + + --transcripts input.fa + + --est_method $method.est_method + #if $method.est_method == "RSEM" or $method.est_method == "eXpress": + --aln_method $method.aln_method + #else if $method.est_method == "salmon": + --salmon_idx_type $method.salmon_idx_type + #end if + + #if $inputs.paired_or_single == "paired": + + #if $inputs.left_input.is_of_type('fasta'): + --left paired_left.fa --right paired_right.fa --seqType fa + #else: + --left paired_left.fq --right paired_right.fq --seqType fq + #end if + + #if $inputs.strand.is_strand_specific: + --SS_lib_type $inputs.strand.library_type + #end if + + --max_ins_size $inputs.paired_fragment_length + + #else: + #if $inputs.input.is_of_type('fasta'): + --single single.fa --seqType fa + #else: + --single single.fq --seqType fq + #end if + + #if $inputs.strand.is_strand_specific: + --SS_lib_type $inputs.strand.library_type + #end if + #end if + + ## Additional parameters. + #if $additional_params.gene_map.has_gene_map == "no": + --gene_trans_map $additional_params.gene_map.gene_trans_map + #else + --trinity_mode + #end if + + --prep_reference + + --output_dir output + + ## CPU + --thread_count \${GALAXY_SLOTS:-4} + ]]></command> + <inputs> + <param format="fasta" name="transcripts" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/> + <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,fastqsanger" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/> + <param format="fasta,fastqsanger" name="right_input" argument="--right" type="data" label="Right/Reverse strand 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="FR">Forward-Reverse</option> + <option value="RF">Reverse-Forward</option> + </param> + </when> + </conditional> + <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/> + </when> + <when value="single"> + <param format="fasta,fastqsanger" argument="--single" name="input" type="data" 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> + </conditional> + + <conditional name="method"> + <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> + <option value="RSEM">RSEM</option> + <option value="eXpress">eXpress</option> + <option value="salmon">Salmon</option> + </param> + <when value="RSEM"> + <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> + <option value="bowtie">Bowtie</option> + <option value="bowtie2">Bowtie2</option> + </param> + </when> + <when value="eXpress"> + <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> + <option value="bowtie">Bowtie</option> + <option value="bowtie2">Bowtie2</option> + </param> + </when> + <when value="salmon"> + <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type"> + <option value="quasi">Quasi</option> + <option value="fmd">FMD</option> + </param> + </when> + </conditional> + + <section name="additional_params" title="Additional Options" expanded="False"> + <conditional name="gene_map"> + <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + </when> + <when value="no"> + <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" /> + </when> + </conditional> + + </section> + </inputs> + <outputs> + <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/RSEM.isoforms.results"> + <filter>method['est_method'] == "RSEM"</filter> + </data> + <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/RSEM.genes.results"> + <filter>method['est_method'] == "RSEM"</filter> + </data> + + <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/results.xprs"> + <filter>method['est_method'] == "eXpress"</filter> + </data> + <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/results.xprs.genes"> + <filter>method['est_method'] == "eXpress"</filter> + </data> + + <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf"> + <filter>method['est_method'] == "salmon"</filter> + </data> + <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes"> + <filter>method['est_method'] == "salmon"</filter> + </data> + </outputs> + <tests> + <test> + <param name="paired_or_single" value="paired"/> + <param name="left_input" value="reads.left.fq"/> + <param name="right_input" value="reads.right.fq"/> + <param name="transcripts" value="raw/Trinity.fasta"/> + <param name="library_type" value="RF"/> + <param name="est_method" value="RSEM"/> + <param name="aln_method" value="bowtie"/> + <param name="has_gene_map" value="yes"/> + <output name="isoforms_counts_rsem"> + <assert_contents> + <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> + <has_n_columns n="8" /> + </assert_contents> + </output> + <output name="genes_counts_rsem"> + <assert_contents> + <has_line_matching expression="TRINITY_DN0_c0_g1	.*" /> + <has_n_columns n="7" /> + </assert_contents> + </output> + </test> + <test> + <param name="paired_or_single" value="paired"/> + <param name="left_input" value="reads.left.fq"/> + <param name="right_input" value="reads.right.fq"/> + <param name="transcripts" value="raw/Trinity.fasta"/> + <param name="library_type" value="RF"/> + <param name="est_method" value="RSEM"/> + <param name="aln_method" value="bowtie2"/> + <param name="has_gene_map" value="yes"/> + <output name="isoforms_counts_rsem"> + <assert_contents> + <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> + <has_n_columns n="8" /> + </assert_contents> + </output> + <output name="genes_counts_rsem"> + <assert_contents> + <has_line_matching expression="TRINITY_DN0_c0_g1	.*" /> + <has_n_columns n="7" /> + </assert_contents> + </output> + </test> + <test> + <param name="paired_or_single" value="paired"/> + <param name="left_input" value="reads.left.fq"/> + <param name="right_input" value="reads.right.fq"/> + <param name="transcripts" value="raw/Trinity.fasta"/> + <param name="library_type" value="RF"/> + <param name="est_method" value="eXpress"/> + <param name="aln_method" value="bowtie"/> + <param name="has_gene_map" value="yes"/> + <output name="isoforms_counts_express"> + <assert_contents> + <has_line_matching expression=".*	TRINITY_DN2_c3_g1_i1	.*" /> + <has_n_columns n="15" /> + </assert_contents> + </output> + <output name="genes_counts_express"> + <assert_contents> + <has_line_matching expression="NA	TRINITY_DN3_c0_g1.*" /> + <has_n_columns n="15" /> + </assert_contents> + </output> + </test> + <test> + <param name="paired_or_single" value="paired"/> + <param name="left_input" value="reads.left.fq"/> + <param name="right_input" value="reads.right.fq"/> + <param name="transcripts" value="raw/Trinity.fasta"/> + <param name="library_type" value="RF"/> + <param name="est_method" value="salmon"/> + <param name="aln_method" value="bowtie"/> + <param name="has_gene_map" value="yes"/> + <output name="isoforms_counts_salmon"> + <assert_contents> + <has_line_matching expression="TRINITY_DN2_c3_g1_i1	.*" /> + <has_n_columns n="5" /> + </assert_contents> + </output> + <output name="genes_counts_salmon"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1.*" /> + <has_n_columns n="5" /> + </assert_contents> + </output> + </test> + </tests> + <help> +<![CDATA[ +Trinity_ assembles transcript sequences from Illumina RNA-Seq data. +This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample. + +**Inputs** + +It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample. +You have to choose between several counting methods. + +If you dont align on a Trinity assembly, you need to provide a file of the following (tabular) format to map gene ids to transcript ids: + +=========== ================ +gene1 transcript1 +----------- ---------------- +gene2 transcript2 +=========== ================ + +**Output** + +This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page: + +.. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification + + +.. _Trinity: http://trinityrnaseq.github.io +]]> + </help> + + <expand macro="citation" /> +</tool>