Mercurial > repos > iuc > trinity
diff abundance_estimates_to_matrix.xml @ 2:de0af39266ef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
| author | iuc |
|---|---|
| date | Mon, 25 Apr 2016 10:02:37 -0400 |
| parents | |
| children | c7555bc21812 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundance_estimates_to_matrix.xml Mon Apr 25 10:02:37 2016 -0400 @@ -0,0 +1,206 @@ +<tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1"> + <description>for a de novo assembly of RNA-Seq data by Trinity</description> + <requirements> + <requirement type="package" version="2.1.1">trinity</requirement> + <requirement type="package" version="1.1.2">bowtie</requirement> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="3.12.0">edger</requirement> + <requirement type="package" version="3.12.0">bioconductor-edger</requirement> + <requirement type="package" version="1.2.28">rsem</requirement> + </requirements> + <stdio> + <exit_code range="1:"/> + </stdio> + <command><![CDATA[ + #for $entry in $samples: + ln -s "${entry.file}" "${entry.sample_name}.tsv" && + #end for + + abundance_estimates_to_matrix.pl + + --est_method ${est_method} + --cross_sample_norm ${additional_params.cross_sample_norm} + + #for $entry in $samples: + "${entry.sample_name}.tsv" + #end for + ]]></command> + <inputs> + <repeat name="samples" title="RSEM abundance estimates for samples"> + <param name="file" label="Add file" type="data" format="tabular"/> + <param name="sample_name" label="Sample name" type="text"> + <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> + </param> + </repeat> + + <param type="select" name="est_method" label="Abundance estimation method"> + <option value="RSEM">RSEM</option> + <option value="eXpress">eXpress</option> + </param> + + <section name="additional_params" title="Additional Options" expanded="False"> + <param type="select" name="cross_sample_norm" label="Cross sample normalization"> + <option value="TMM">TMM</option> + <option value="UpperQuartile">UpperQuartile</option> + <option value="none">None</option> + </param> + </section> + </inputs> + <outputs> + <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/> + <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/> + <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix"> + <filter>additional_params['cross_sample_norm'] == "TMM"</filter> + </data> + <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix"> + <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter> + </data> + </outputs> + <tests> + <test> + <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> + <param name="samples_0|sample_name" value="sample_A"/> + <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/> + <param name="samples_1|sample_name" value="sample_B"/> + <param name="est_method" value="RSEM"/> + <param name="cross_sample_norm" value="TMM"/> + <output name="trans_counts"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="TPM_no_norm"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="norm"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + </test> + <test> + <param name="samples_0|file" value="count/rsem_bowtie2/RSEM.genes.results"/> + <param name="samples_0|sample_name" value="sample_A"/> + <param name="samples_1|file" value="count/rsem_bowtie2/RSEM.genes_B.results"/> + <param name="samples_1|sample_name" value="sample_B"/> + <param name="est_method" value="RSEM"/> + <param name="cross_sample_norm" value="TMM"/> + <output name="trans_counts"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="TPM_no_norm"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="norm"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + </test> + <test> + <param name="samples_0|file" value="count/express_bowtie/results.xprs.genes"/> + <param name="samples_0|sample_name" value="sample_A"/> + <param name="samples_1|file" value="count/express_bowtie/results_B.xprs.genes"/> + <param name="samples_1|sample_name" value="sample_B"/> + <param name="est_method" value="eXpress"/> + <param name="cross_sample_norm" value="TMM"/> + <output name="trans_counts"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="TPM_no_norm"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="norm"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + </test> + <test> + <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> + <param name="samples_0|sample_name" value="sample_A"/> + <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/> + <param name="samples_1|sample_name" value="sample_B"/> + <param name="est_method" value="RSEM"/> + <param name="cross_sample_norm" value="UpperQuartile"/> + <output name="trans_counts"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="TPM_no_norm"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="norm" file="count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix" /> + </test> + <test> + <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> + <param name="samples_0|sample_name" value="sample_A"/> + <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/> + <param name="samples_1|sample_name" value="sample_B"/> + <param name="est_method" value="RSEM"/> + <param name="cross_sample_norm" value="none"/> + <output name="trans_counts"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="TPM_no_norm"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + </test> + </tests> + <help> +<![CDATA[ +Trinity_ assembles transcript sequences from Illumina RNA-Seq data. +This tool will combine abundance estimations (produced by 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool) from multiple samples into a single tabular file. +This matrix can then be used by 'RNASeq samples quality check for transcript quantification' and 'Differential Expression Analysis using a Trinity assembly' tools. + +**Inputs** + +It takes as input multiple results from 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool/ +Each sample must have a name, that should be used in subsequent tools. + +**Output** + +This tool will produce a single matrix file. More details on this page: + +.. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification + + +.. _Trinity: http://trinityrnaseq.github.io +]]> + </help> + + <citations> + <citation type="doi">doi:10.1038/nbt.1883</citation> + </citations> +</tool> +