Mercurial > repos > yhoogstrate > edger_with_design_matrix
diff edgeR_Concatenate_Expression_Matrices.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 | f06dceb5b966 |
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--- a/edgeR_Concatenate_Expression_Matrices.xml Tue Sep 01 04:32:16 2015 -0400 +++ b/edgeR_Concatenate_Expression_Matrices.xml Tue Sep 01 04:45:24 2015 -0400 @@ -1,168 +1,172 @@ <?xml version="1.0" encoding="UTF-8"?> <tool id="concatenate_expression_matrices" name="edgeR: Concatenate Expression Matrices" version="1.0.0"> - <description>Create a full expression matrix by selecting the desired columns from specific count tables</description> - - <command> - #set $j = 0 - #set $paste = [] - - #if $add_geneids.choice == "true": - #set $filename = str($j)+".txt" - #set paste = paste + [$filename] - - cut -f $add_geneids.column_geneids.value "$add_geneids.sample_geneids" > $filename ; - #set $j += 1 - #end if - - #for $sample in $samples: - ##echo "$sample.column_index" - ##echo "$sample.column_index.value" - - #set $column_str = ",".join([str(x).strip() for x in $sample.column_index.value]) - #set $filename = str($j)+".txt" - #set paste = paste + [$filename] - - cut -f "$column_str" "$sample.sample" > $filename ; - #set $j += 1 - #end for - - #if $add_lengths.choice == "true": - #set $filename = str($j)+".txt" - #set paste = paste + [$filename] - - cut -f $add_lengths.column_lengths.value "$add_lengths.sample_lengths" > $filename ; - #set $j += 1 - #end if - - #set $paste_str = " ".join([str(x).strip() for x in $paste]) - - paste $paste_str > $expression_matrix - </command> - - <inputs> - <conditional name="add_geneids"> - <param name="choice" type="select" label="Add a gene-IDs column at the end of the file" help="Highly recommended to select!" > - <option value="false">No</option> - <option value="true" selected="true">Yes</option> - </param> - <when value="false" /> - <when value="true"> - <param name="sample_geneids" type="data" format="tabular" label="Select Read-count dataset that contains a column for GeneIDs" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." /> - <param name="column_geneids" numerical="false" use_header_names="true" label="Select GeneID column" type="data_column" data_ref="sample_geneids" multiple="false"> - <validator type="no_options" message="Please select at least one column." /> - </param> - </when> - </conditional> - - <repeat name="samples" title="Expression Table" help="E.g. a earlier concatenated table, or a HT-seq, featureCounts or DESeq-count result."> - <param name="sample" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." /> - <!-- select columns --> - <param name="column_index" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="sample" multiple="true" size="120" display="checkboxes"> - <validator type="no_options" message="Please select at least one column." /> - </param> - </repeat> - - <conditional name="add_lengths"> - <param name="choice" type="select" label="Add a gene-lengths column at the end of the file" help="Optional, only usefull if RPKM/FPKM calculation is desired." > - <option value="false">No</option> - <option value="true">Yes</option> - </param> - <when value="false" /> - <when value="true"> - <param name="sample_lengths" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." /> - <param name="column_lengths" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="sample_lengths" multiple="false" size="120"> - <validator type="no_options" message="Please select at least one column." /> - </param> - </when> - </conditional> - - <param name="remove_comment_lines" type="boolean" label="Automatically remove 'comment' lines starting with a '#'" truevale="true" falsevalue="false" selected="true" help="Some tools (incl. featureCounts) include comment lines that are not neccesairy for downstream analyis. By enabling this function, these lines will be removed." /> - - </inputs> - - <outputs> - <data format="tabular" name="expression_matrix" label="Expression matrix" /> - </outputs> - - <tests> - <test> - <conditional name="add_geneids"> - <param name="choice" value="true" /> - <param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" /> - <param name="column_geneids" value="1" /> - </conditional> - - <param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" /> - <param name="samples_0|column_index" value="2" /> - - <conditional name="add_lengths"> - <param name="choice" value="false" /> - </conditional> - - <param name="remove_comment_lines" value="false" /> - - <output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_Control_1.txt" /> - </test> - <test> - <conditional name="add_geneids"> - <param name="choice" value="true" /> - <param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" /> - <param name="column_geneids" value="1" /> - </conditional> - - <!-- <repeat name="samples"> --> - <param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" /> - <param name="samples_0|column_index" value="2" /> - <!-- </repeat> --> - - <!-- <repeat name="samples"> --> - <param name="samples_1|sample" value="GSE51403/GSE51403_expression_matrix_Control_2.txt" /> - <param name="samples_1|column_index" value="2" /> - <!-- </repeat> --> - - <!-- <repeat name="samples"> --> - <param name="samples_2|sample" value="GSE51403/GSE51403_expression_matrix_Control_3.txt" /> - <param name="samples_2|column_index" value="2" /> - <!-- </repeat> --> - - <!-- <repeat name="samples"> --> - <param name="samples_3|sample" value="GSE51403/GSE51403_expression_matrix_Control_4.txt" /> - <param name="samples_3|column_index" value="2" /> - <!-- </repeat> --> - - <!-- <repeat name="samples"> --> - <param name="samples_4|sample" value="GSE51403/GSE51403_expression_matrix_Control_5.txt" /> - <param name="samples_4|column_index" value="2" /> - <!-- </repeat> --> - - <!-- <repeat name="samples"> --> - <param name="samples_5|sample" value="GSE51403/GSE51403_expression_matrix_Control_6.txt" /> - <param name="samples_5|column_index" value="2" /> - <!-- </repeat> --> - - <!-- <repeat name="samples"> --> - <param name="samples_6|sample" value="GSE51403/GSE51403_expression_matrix_Control_7.txt" /> - <param name="samples_6|column_index" value="2" /> - <!-- </repeat> --> - - <!-- <repeat name="samples"> --> - <param name="samples_7|sample" value="GSE51403/GSE51403_expression_matrix_E2.txt" /> - <param name="samples_7|column_index" value="2,3,4,5,6,7,8" /> - <!-- </repeat> --> - - <conditional name="add_lengths"> - <param name="choice" value="true" /> - <param name="sample_lengths" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" /> - <param name="column_lengths" value="2" /> - </conditional> - - <param name="remove_comment_lines" value="false" /> - - <output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_full.txt" /> - </test> - </tests> - - <help> + <description>Create a full expression matrix by selecting the desired columns from specific count tables</description> + + <macros> + <import>edgeR_macros.xml</import> + </macros> + + <command> + #set $j = 0 + #set $paste = [] + + #if $add_geneids.choice == "true": + #set $filename = str($j)+".txt" + #set paste = paste + [$filename] + + cut -f $add_geneids.column_geneids.value "$add_geneids.sample_geneids" > $filename ; + #set $j += 1 + #end if + + #for $sample in $samples: + ##echo "$sample.column_index" + ##echo "$sample.column_index.value" + + #set $column_str = ",".join([str(x).strip() for x in $sample.column_index.value]) + #set $filename = str($j)+".txt" + #set paste = paste + [$filename] + + cut -f "$column_str" "$sample.sample" > $filename ; + #set $j += 1 + #end for + + #if $add_lengths.choice == "true": + #set $filename = str($j)+".txt" + #set paste = paste + [$filename] + + cut -f $add_lengths.column_lengths.value "$add_lengths.sample_lengths" > $filename ; + #set $j += 1 + #end if + + #set $paste_str = " ".join([str(x).strip() for x in $paste]) + + paste $paste_str > $expression_matrix + </command> + + <inputs> + <conditional name="add_geneids"> + <param name="choice" type="select" label="Add a gene-IDs column at the end of the file" help="Highly recommended to select!" > + <option value="false">No</option> + <option value="true" selected="true">Yes</option> + </param> + <when value="false" /> + <when value="true"> + <param name="sample_geneids" type="data" format="tabular" label="Select Read-count dataset that contains a column for GeneIDs" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." /> + <param name="column_geneids" numerical="false" use_header_names="true" label="Select GeneID column" type="data_column" data_ref="sample_geneids" multiple="false"> + <validator type="no_options" message="Please select at least one column." /> + </param> + </when> + </conditional> + + <repeat name="samples" title="Expression Table" help="E.g. a earlier concatenated table, or a HT-seq, featureCounts or DESeq-count result."> + <param name="sample" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." /> + <!-- select columns --> + <param name="column_index" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="sample" multiple="true" size="120" display="checkboxes"> + <validator type="no_options" message="Please select at least one column." /> + </param> + </repeat> + + <conditional name="add_lengths"> + <param name="choice" type="select" label="Add a gene-lengths column at the end of the file" help="Optional, only usefull if RPKM/FPKM calculation is desired." > + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false" /> + <when value="true"> + <param name="sample_lengths" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." /> + <param name="column_lengths" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="sample_lengths" multiple="false" size="120"> + <validator type="no_options" message="Please select at least one column." /> + </param> + </when> + </conditional> + + <param name="remove_comment_lines" type="boolean" label="Automatically remove 'comment' lines starting with a '#'" truevale="true" falsevalue="false" selected="true" help="Some tools (incl. featureCounts) include comment lines that are not neccesairy for downstream analyis. By enabling this function, these lines will be removed." /> + + </inputs> + + <outputs> + <data format="tabular" name="expression_matrix" label="Expression matrix" /> + </outputs> + + <tests> + <test> + <conditional name="add_geneids"> + <param name="choice" value="true" /> + <param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" /> + <param name="column_geneids" value="1" /> + </conditional> + + <param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" /> + <param name="samples_0|column_index" value="2" /> + + <conditional name="add_lengths"> + <param name="choice" value="false" /> + </conditional> + + <param name="remove_comment_lines" value="false" /> + + <output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_Control_1.txt" /> + </test> + <test> + <conditional name="add_geneids"> + <param name="choice" value="true" /> + <param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" /> + <param name="column_geneids" value="1" /> + </conditional> + + <!-- <repeat name="samples"> --> + <param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" /> + <param name="samples_0|column_index" value="2" /> + <!-- </repeat> --> + + <!-- <repeat name="samples"> --> + <param name="samples_1|sample" value="GSE51403/GSE51403_expression_matrix_Control_2.txt" /> + <param name="samples_1|column_index" value="2" /> + <!-- </repeat> --> + + <!-- <repeat name="samples"> --> + <param name="samples_2|sample" value="GSE51403/GSE51403_expression_matrix_Control_3.txt" /> + <param name="samples_2|column_index" value="2" /> + <!-- </repeat> --> + + <!-- <repeat name="samples"> --> + <param name="samples_3|sample" value="GSE51403/GSE51403_expression_matrix_Control_4.txt" /> + <param name="samples_3|column_index" value="2" /> + <!-- </repeat> --> + + <!-- <repeat name="samples"> --> + <param name="samples_4|sample" value="GSE51403/GSE51403_expression_matrix_Control_5.txt" /> + <param name="samples_4|column_index" value="2" /> + <!-- </repeat> --> + + <!-- <repeat name="samples"> --> + <param name="samples_5|sample" value="GSE51403/GSE51403_expression_matrix_Control_6.txt" /> + <param name="samples_5|column_index" value="2" /> + <!-- </repeat> --> + + <!-- <repeat name="samples"> --> + <param name="samples_6|sample" value="GSE51403/GSE51403_expression_matrix_Control_7.txt" /> + <param name="samples_6|column_index" value="2" /> + <!-- </repeat> --> + + <!-- <repeat name="samples"> --> + <param name="samples_7|sample" value="GSE51403/GSE51403_expression_matrix_E2.txt" /> + <param name="samples_7|column_index" value="2,3,4,5,6,7,8" /> + <!-- </repeat> --> + + <conditional name="add_lengths"> + <param name="choice" value="true" /> + <param name="sample_lengths" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" /> + <param name="column_lengths" value="2" /> + </conditional> + + <param name="remove_comment_lines" value="false" /> + + <output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_full.txt" /> + </test> + </tests> + + <help> edgeR: Concatenate Expression Matrices ####################################### @@ -179,28 +183,8 @@ Input ----- - -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>