Mercurial > repos > iuc > trinity
comparison run_DE_analysis.xml @ 4:692491de7df5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
| author | iuc |
|---|---|
| date | Thu, 12 May 2016 07:02:10 -0400 |
| parents | c7555bc21812 |
| children | e4a9e0798360 |
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| 3:c7555bc21812 | 4:692491de7df5 |
|---|---|
| 1 <tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1"> | 1 <tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1.1"> |
| 2 <description>using a Trinity assembly</description> | 2 <description>using a Trinity assembly</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="2.1.1">trinity</requirement> | 4 <requirement type="package" version="2.1.1">trinity</requirement> |
| 5 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> | 5 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> |
| 6 <requirement type="package" version="1.10.0">deseq2</requirement> | 6 <requirement type="package" version="1.10.0">deseq2</requirement> |
| 7 <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement> | 7 <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement> |
| 8 <requirement type="package" version="3.12.0">edger</requirement> | 8 <requirement type="package" version="3.12.0">edger</requirement> |
| 9 <requirement type="package" version="3.12.0">bioconductor-edger</requirement> | 9 <requirement type="package" version="3.12.0">bioconductor-edger</requirement> |
| 10 <requirement type="package" version="3.27.4">limma</requirement> | 10 <requirement type="package" version="3.28.2">limma</requirement> |
| 11 <requirement type="package" version="3.27.4">bioconductor-limma</requirement> | 11 <requirement type="package" version="3.27.4">bioconductor-limma</requirement> |
| 12 </requirements> | 12 </requirements> |
| 13 <stdio> | 13 <stdio> |
| 14 <exit_code range="1:"/> | 14 <exit_code range="1:"/> |
| 15 </stdio> | 15 </stdio> |
| 16 <command><![CDATA[ | 16 <command><![CDATA[ |
| 17 | 17 |
| 18 ln -s "${matrix}" "input.matrix" | 18 ln -s "${matrix}" "input.matrix" |
| 19 | 19 |
| 20 && | 20 && |
| 21 | 21 |
| 22 run_DE_analysis.pl | 22 run_DE_analysis.pl |
| 23 | 23 |
| 24 --matrix "input.matrix" | 24 --matrix "input.matrix" |
| 25 | 25 |
| 26 --samples_file "${samples}" | 26 --samples_file "${samples}" |
| 27 | 27 |
| 28 --method ${method_choice.method} | 28 --method ${method_choice.method} |
| 29 | 29 |
| 30 #if $method_choice.method == "edgeR": | 30 #if $method_choice.method == "edgeR": |
| 31 --dispersion ${method_choice.edger_dispersion} | 31 --dispersion ${method_choice.edger_dispersion} |
| 32 #end if | 32 #end if |
| 33 | 33 |
| 34 #if $method_choice.method == "ROTS": | 34 #if $method_choice.method == "ROTS": |
| 35 --ROTS_B ${method_choice.rots_b} | 35 --ROTS_B ${method_choice.rots_b} |
| 36 --ROTS_K ${method_choice.rots_k} | 36 --ROTS_K ${method_choice.rots_k} |
| 37 #end if | 37 #end if |
| 38 | 38 |
| 39 --min_rowSum_counts ${additional_params.min_rowSum_counts} | 39 --min_rowSum_counts ${additional_params.min_rowSum_counts} |
| 40 | 40 |
| 41 #if $additional_params.reference_sample: | 41 #if $additional_params.reference_sample: |
| 42 --reference_sample ${additional_params.reference_sample} | 42 --reference_sample ${additional_params.reference_sample} |
| 43 #end if | 43 #end if |
| 44 | 44 |
| 45 #if $additional_params.contrasts: | 45 #if $additional_params.contrasts: |
| 46 --contrasts ${additional_params.contrasts} | 46 --contrasts ${additional_params.contrasts} |
| 47 #end if | 47 #end if |
| 48 | 48 |
| 49 --output results | 49 --output results |
| 50 | 50 |
| 51 ]]></command> | 51 ]]></command> |
| 52 <inputs> | 52 <inputs> |
| 53 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/> | 53 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/> |
| 54 <param format="tabular" name="samples" type="data" label="Sample description" help="file describing samples and replicates"/> | 54 <param format="tabular" name="samples" type="data" label="Sample description" help="file describing samples and replicates"/> |
| 55 | 55 |
| 56 <conditional name="method_choice"> | 56 <conditional name="method_choice"> |
| 57 <param type="select" name="method" label="Differential analysis method"> | 57 <param type="select" name="method" label="Differential analysis method"> |
| 58 <option value="edgeR">edgeR</option> | 58 <option value="edgeR">edgeR</option> |
| 59 <option value="DESeq2">DESeq2</option> | 59 <option value="DESeq2">DESeq2</option> |
| 60 <option value="voom">voom</option> | 60 <option value="voom">voom</option> |
| 70 <when value="voom"> | 70 <when value="voom"> |
| 71 </when> | 71 </when> |
| 72 <when value="DESeq2"> | 72 <when value="DESeq2"> |
| 73 </when> | 73 </when> |
| 74 </conditional> | 74 </conditional> |
| 75 | 75 |
| 76 <section name="additional_params" title="Additional Options" expanded="False"> | 76 <section name="additional_params" title="Additional Options" expanded="False"> |
| 77 <param name="min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/> | 77 <param name="min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/> |
| 78 <param name="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"/> | 78 <param name="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"/> |
| 79 <param format="tabular" name="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"/> | 79 <param format="tabular" name="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"/> |
| 80 </section> | 80 </section> |
| 136 | 136 |
| 137 | 137 |
| 138 .. _Trinity: http://trinityrnaseq.github.io | 138 .. _Trinity: http://trinityrnaseq.github.io |
| 139 ]]> | 139 ]]> |
| 140 </help> | 140 </help> |
| 141 | 141 |
| 142 <citations> | 142 <citations> |
| 143 <citation type="doi">doi:10.1038/nbt.1883</citation> | 143 <citation type="doi">doi:10.1038/nbt.1883</citation> |
| 144 </citations> | 144 </citations> |
| 145 </tool> | 145 </tool> |
| 146 | 146 |