Mercurial > repos > iuc > trinity_run_de_analysis
diff run_de_analysis.xml @ 5:2a30d7dfe8de draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
| author | iuc |
|---|---|
| date | Fri, 31 Mar 2017 11:33:18 -0400 |
| parents | 7e1c70d4e4a4 |
| children | 0f5bfda8f46c |
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--- a/run_de_analysis.xml Thu Mar 23 10:13:10 2017 -0400 +++ b/run_de_analysis.xml Fri Mar 31 11:33:18 2017 -0400 @@ -1,18 +1,16 @@ -<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.1"> +<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.0"> <description>using a Trinity assembly</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> - <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> - <requirement type="package" version="3.14.0">bioconductor-edger</requirement> - <requirement type="package" version="3.28.10">bioconductor-limma</requirement> - <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement> + <requirement type="package" version="3.16.5">bioconductor-edger</requirement> + <requirement type="package" version="3.30.13">bioconductor-limma</requirement> + <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> </expand> - <expand macro="stdio"/> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ - ln -s "${matrix}" "input.matrix" + ln -f -s "${matrix}" "input.matrix" && @@ -33,7 +31,7 @@ --ROTS_K ${method_choice.rots_k} #end if - --min_rowSum_counts ${additional_params.min_rowSum_counts} + --min_reps_min_cpm ${additional_params.min_reps},${additional_params.min_cpm} #if $additional_params.reference_sample: --reference_sample ${additional_params.reference_sample} @@ -71,7 +69,8 @@ </conditional> <section name="additional_params" title="Additional Options" expanded="False"> - <param name="min_rowSum_counts" argument="--min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/> + <param name="min_cpm" type="integer" value="1" label="Minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/> + <param name="min_reps" type="integer" value="2" label="Minimum number of replicates meeting minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/> <param name="reference_sample" argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/> <param format="tabular" name="contrasts" argument="--contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/> </section> @@ -80,6 +79,9 @@ <collection name="DE_results" type="list" label="Differential expression results on ${on_string}"> <discover_datasets pattern="(?P<name>.+)\.DE_results$" ext="tabular" directory="results" /> </collection> + <collection name="count_matrices" type="list" label="Count matrices generated for differential expression on ${on_string}"> + <discover_datasets pattern="(?P<name>.+)\.count_matrix$" ext="tabular" directory="results" /> + </collection> <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}"> <discover_datasets pattern="(?P<name>.+)\.pdf$" ext="pdf" directory="results" /> </collection> @@ -94,6 +96,11 @@ <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/> <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/> </output_collection> + <output_collection name="count_matrices"> + <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix"/> + <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix"/> + <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix"/> + </output_collection> <output_collection name="PDF_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/> <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> @@ -109,6 +116,11 @@ <element name="input.matrix.wt_37_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results"/> <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results"/> </output_collection> + <output_collection name="count_matrices"> + <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.count_matrix"/> + <element name="input.matrix.wt_37_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.count_matrix"/> + <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.count_matrix"/> + </output_collection> <output_collection name="PDF_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf"/> <element name="input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/> @@ -124,6 +136,11 @@ <element name="input.matrix.wt_37_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results"/> <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results"/> </output_collection> + <output_collection name="count_matrices"> + <element name="input.matrix.wt_37_vs_wt_GSNO.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.count_matrix"/> + <element name="input.matrix.wt_37_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.count_matrix"/> + <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix"/> + </output_collection> <output_collection name="PDF_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf"/> <element name="input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf"/>