Mercurial > repos > yhoogstrate > edger_with_design_matrix
diff edgeR_Design_from_Expression_Matrix.xml @ 108:a02794bb9073 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
| author | yhoogstrate |
|---|---|
| date | Tue, 01 Sep 2015 04:45:24 -0400 |
| parents | 450c1c9a2938 |
| children | dfebd3787276 |
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--- a/edgeR_Design_from_Expression_Matrix.xml Tue Sep 01 04:32:16 2015 -0400 +++ b/edgeR_Design_from_Expression_Matrix.xml Tue Sep 01 04:45:24 2015 -0400 @@ -1,119 +1,123 @@ <?xml version="1.0" encoding="UTF-8"?> <tool id="design_from_expression_matrix" name="edgeR: Design- from Expression matrix" version="1.0.0.a"> - <description>Create design- from an expression matrix</description> - - <requirements> - <requirement type="package" version="1.0.0">design_matrix_creator</requirement> - </requirements> - - <command interpreter="python"> - design_matrix_creator - -c $expression_matrix - - #set $unique_columns = [] - #for $factor in $treatments: - #for $level in $factor.rep_factorLevel: - #for $val in $level.factorIndex.value: - #if str($val) not in $unique_columns: - #set $unique_columns = $unique_columns + [str($val)] - #end if - #end for - #end for - #end for - - #set $unique_columns = " ".join(unique_columns) - -s $unique_columns - - -t - #for $factor in $treatments: - #set $factor_str = str($factor.name).encode('base64').replace('\n','') - - #for $level in $factor.rep_factorLevel: - #set $factor_str = $factor_str+":"+str($level.factorLevel).encode('base64').replace('\n','')+":"+",".join([str(x).strip() for x in $level.factorIndex.value]) - #end for - - $factor_str - #end for - - #if $choose_blocking.choice == "true" - -b - #for blocking in $choose_blocking.blocking_repeat: - #set $blocking_str = str($blocking.blocking_name).encode('base64').replace('\n','') - - #for $block_iter in $blocking.block: - #set $block_str = ",".join([str(x).strip() for x in $block_iter.block_index.value]) - #set $blocking_str = $blocking_str+":"+$block_str - #end for - - $blocking_str - #end for - #end if - - -o $design_matrix - </command> - - <inputs> - <param format="tabular" name="expression_matrix" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" /> - - <repeat name="treatments" title="Factor/Condition" min="1"> - <param name="name" type="text" value="FactorName" label="Specify a name for the factor / condition" help="e.g. 'Tumor vs. Normal', 'Timepoint' or 'DiseaseState'. Field must be non-numerical, preferably only letters!!" /> - <repeat name="rep_factorLevel" title="Factor level" min="1"> - <param name="factorLevel" type="text" value="FactorLevel" label="Specify a condition" help="e.g. Tumor or Normal; Treated, untreaded or placebo. Field must be non-numerical, preferably only letters!!" /> - <param name="factorIndex" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="expression_matrix" multiple="true" size="120" display="checkboxes"> - <validator type="no_options" message="Please select at least one column." /> - </param> - </repeat> - </repeat> - - <conditional name="choose_blocking"> - <param name="choice" type="select" label="Define blocking (paired or grouped samples)" help="e.g. to remove batch effects" > - <option value="false">No</option> - <option value="true">Yes</option> - </param> - <when value="false" /> - <when value="true"> - <repeat name="blocking_repeat" title="Blocking condition" min="1"> - <param name="blocking_name" type="text" value="" label="Specify a name for a blocking condition" help="e.g.'Patients' or 'Batches'" /> - <repeat name="block" title="Block" min="2"> - <param name="block_index" label="Select columns that are associated with this factor level" type="data_column" data_ref="expression_matrix" numerical="True" multiple="true" use_header_names="true" size="120" display="checkboxes"> - <validator type="no_options" message="Please select at least one column." /> - </param> - </repeat> - </repeat> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="design_matrix" label="Design matrix" /> - </outputs> - - - <tests> - <test> - <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" /> - - <!-- <repeat name="treatments"> --> - <param name="treatments_0|name" value="Treatment" /> - <!-- <repeat name="rep_factorLevel"> --> - <param name="treatments_0|rep_factorLevel_0|factorLevel" value="Control" /> - <param name="treatments_0|rep_factorLevel_0|factorIndex" value="2,3,4,5,6,7,8" /> - <!-- </repeat> --> - <!-- <repeat name="rep_factorLevel"> --> - <param name="treatments_0|rep_factorLevel_1|factorLevel" value="E2" /> - <param name="treatments_0|rep_factorLevel_1|factorIndex" value="9,10,11,12,13,14,15" /> - <!-- </repeat> --> - <!-- </repeat> --> - - <conditional name="choose_blocking"> - <param value="false" /> - </conditional> - - <output name="design_matrix" file="GSE51403/GSE51403_design_matrix_full_depth.txt" /> - </test> - </tests> - - <help> + <description>Create design- from an expression matrix</description> + + <macros> + <import>edgeR_macros.xml</import> + </macros> + + <requirements> + <requirement type="package" version="1.0.0">design_matrix_creator</requirement> + </requirements> + + <command interpreter="python"> + design_matrix_creator + -c $expression_matrix + + #set $unique_columns = [] + #for $factor in $treatments: + #for $level in $factor.rep_factorLevel: + #for $val in $level.factorIndex.value: + #if str($val) not in $unique_columns: + #set $unique_columns = $unique_columns + [str($val)] + #end if + #end for + #end for + #end for + + #set $unique_columns = " ".join(unique_columns) + -s $unique_columns + + -t + #for $factor in $treatments: + #set $factor_str = str($factor.name).encode('base64').replace('\n','') + + #for $level in $factor.rep_factorLevel: + #set $factor_str = $factor_str+":"+str($level.factorLevel).encode('base64').replace('\n','')+":"+",".join([str(x).strip() for x in $level.factorIndex.value]) + #end for + + $factor_str + #end for + + #if $choose_blocking.choice == "true" + -b + #for blocking in $choose_blocking.blocking_repeat: + #set $blocking_str = str($blocking.blocking_name).encode('base64').replace('\n','') + + #for $block_iter in $blocking.block: + #set $block_str = ",".join([str(x).strip() for x in $block_iter.block_index.value]) + #set $blocking_str = $blocking_str+":"+$block_str + #end for + + $blocking_str + #end for + #end if + + -o $design_matrix + </command> + + <inputs> + <param format="tabular" name="expression_matrix" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" /> + + <repeat name="treatments" title="Factor/Condition" min="1"> + <param name="name" type="text" value="FactorName" label="Specify a name for the factor / condition" help="e.g. 'Tumor vs. Normal', 'Timepoint' or 'DiseaseState'. Field must be non-numerical, preferably only letters!!" /> + <repeat name="rep_factorLevel" title="Factor level" min="1"> + <param name="factorLevel" type="text" value="FactorLevel" label="Specify a condition" help="e.g. Tumor or Normal; Treated, untreaded or placebo. Field must be non-numerical, preferably only letters!!" /> + <param name="factorIndex" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="expression_matrix" multiple="true" size="120" display="checkboxes"> + <validator type="no_options" message="Please select at least one column." /> + </param> + </repeat> + </repeat> + + <conditional name="choose_blocking"> + <param name="choice" type="select" label="Define blocking (paired or grouped samples)" help="e.g. to remove batch effects" > + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false" /> + <when value="true"> + <repeat name="blocking_repeat" title="Blocking condition" min="1"> + <param name="blocking_name" type="text" value="" label="Specify a name for a blocking condition" help="e.g.'Patients' or 'Batches'" /> + <repeat name="block" title="Block" min="2"> + <param name="block_index" label="Select columns that are associated with this factor level" type="data_column" data_ref="expression_matrix" numerical="True" multiple="true" use_header_names="true" size="120" display="checkboxes"> + <validator type="no_options" message="Please select at least one column." /> + </param> + </repeat> + </repeat> + </when> + </conditional> + </inputs> + + <outputs> + <data format="tabular" name="design_matrix" label="Design matrix" /> + </outputs> + + + <tests> + <test> + <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" /> + + <!-- <repeat name="treatments"> --> + <param name="treatments_0|name" value="Treatment" /> + <!-- <repeat name="rep_factorLevel"> --> + <param name="treatments_0|rep_factorLevel_0|factorLevel" value="Control" /> + <param name="treatments_0|rep_factorLevel_0|factorIndex" value="2,3,4,5,6,7,8" /> + <!-- </repeat> --> + <!-- <repeat name="rep_factorLevel"> --> + <param name="treatments_0|rep_factorLevel_1|factorLevel" value="E2" /> + <param name="treatments_0|rep_factorLevel_1|factorIndex" value="9,10,11,12,13,14,15" /> + <!-- </repeat> --> + <!-- </repeat> --> + + <conditional name="choose_blocking"> + <param value="false" /> + </conditional> + + <output name="design_matrix" file="GSE51403/GSE51403_design_matrix_full_depth.txt" /> + </test> + </tests> + + <help> edgeR: Design- from Expression matrix ##################################### @@ -131,27 +135,8 @@ The test data is coming from: doi: 10.1093/bioinformatics/btt688. http://www.ncbi.nlm.nih.gov/pubmed/24319002 -Contact -------- - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands) on behalf of the Translational -Research IT (TraIT) project: - -http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch - -More tools by the Translational Research IT (TraIT) project can be found -in the following toolsheds: - -http://toolshed.dtls.nl/ - -http://toolshed.g2.bx.psu.edu - -http://testtoolshed.g2.bx.psu.edu/ - </help> - - <citations> - <citation type="doi">10.1093/bioinformatics/btp616</citation> - <citation type="doi">10.1093/bioinformatics/btt688</citation> - </citations> +@CONTACT@ + </help> + + <expand macro="citations" /> </tool>