Mercurial > repos > yhoogstrate > edger_with_design_matrix
comparison 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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| 107:049d8bc2214e | 108:a02794bb9073 |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
| 2 <tool id="design_from_expression_matrix" name="edgeR: Design- from Expression matrix" version="1.0.0.a"> | 2 <tool id="design_from_expression_matrix" name="edgeR: Design- from Expression matrix" version="1.0.0.a"> |
| 3 <description>Create design- from an expression matrix</description> | 3 <description>Create design- from an expression matrix</description> |
| 4 | 4 |
| 5 <requirements> | 5 <macros> |
| 6 <requirement type="package" version="1.0.0">design_matrix_creator</requirement> | 6 <import>edgeR_macros.xml</import> |
| 7 </requirements> | 7 </macros> |
| 8 | 8 |
| 9 <command interpreter="python"> | 9 <requirements> |
| 10 design_matrix_creator | 10 <requirement type="package" version="1.0.0">design_matrix_creator</requirement> |
| 11 -c $expression_matrix | 11 </requirements> |
| 12 | 12 |
| 13 #set $unique_columns = [] | 13 <command interpreter="python"> |
| 14 #for $factor in $treatments: | 14 design_matrix_creator |
| 15 #for $level in $factor.rep_factorLevel: | 15 -c $expression_matrix |
| 16 #for $val in $level.factorIndex.value: | 16 |
| 17 #if str($val) not in $unique_columns: | 17 #set $unique_columns = [] |
| 18 #set $unique_columns = $unique_columns + [str($val)] | 18 #for $factor in $treatments: |
| 19 #end if | 19 #for $level in $factor.rep_factorLevel: |
| 20 #end for | 20 #for $val in $level.factorIndex.value: |
| 21 #end for | 21 #if str($val) not in $unique_columns: |
| 22 #end for | 22 #set $unique_columns = $unique_columns + [str($val)] |
| 23 | 23 #end if |
| 24 #set $unique_columns = " ".join(unique_columns) | 24 #end for |
| 25 -s $unique_columns | 25 #end for |
| 26 | 26 #end for |
| 27 -t | 27 |
| 28 #for $factor in $treatments: | 28 #set $unique_columns = " ".join(unique_columns) |
| 29 #set $factor_str = str($factor.name).encode('base64').replace('\n','') | 29 -s $unique_columns |
| 30 | 30 |
| 31 #for $level in $factor.rep_factorLevel: | 31 -t |
| 32 #set $factor_str = $factor_str+":"+str($level.factorLevel).encode('base64').replace('\n','')+":"+",".join([str(x).strip() for x in $level.factorIndex.value]) | 32 #for $factor in $treatments: |
| 33 #end for | 33 #set $factor_str = str($factor.name).encode('base64').replace('\n','') |
| 34 | 34 |
| 35 $factor_str | 35 #for $level in $factor.rep_factorLevel: |
| 36 #end for | 36 #set $factor_str = $factor_str+":"+str($level.factorLevel).encode('base64').replace('\n','')+":"+",".join([str(x).strip() for x in $level.factorIndex.value]) |
| 37 | 37 #end for |
| 38 #if $choose_blocking.choice == "true" | 38 |
| 39 -b | 39 $factor_str |
| 40 #for blocking in $choose_blocking.blocking_repeat: | 40 #end for |
| 41 #set $blocking_str = str($blocking.blocking_name).encode('base64').replace('\n','') | 41 |
| 42 | 42 #if $choose_blocking.choice == "true" |
| 43 #for $block_iter in $blocking.block: | 43 -b |
| 44 #set $block_str = ",".join([str(x).strip() for x in $block_iter.block_index.value]) | 44 #for blocking in $choose_blocking.blocking_repeat: |
| 45 #set $blocking_str = $blocking_str+":"+$block_str | 45 #set $blocking_str = str($blocking.blocking_name).encode('base64').replace('\n','') |
| 46 #end for | 46 |
| 47 | 47 #for $block_iter in $blocking.block: |
| 48 $blocking_str | 48 #set $block_str = ",".join([str(x).strip() for x in $block_iter.block_index.value]) |
| 49 #end for | 49 #set $blocking_str = $blocking_str+":"+$block_str |
| 50 #end if | 50 #end for |
| 51 | 51 |
| 52 -o $design_matrix | 52 $blocking_str |
| 53 </command> | 53 #end for |
| 54 | 54 #end if |
| 55 <inputs> | 55 |
| 56 <param format="tabular" name="expression_matrix" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" /> | 56 -o $design_matrix |
| 57 | 57 </command> |
| 58 <repeat name="treatments" title="Factor/Condition" min="1"> | 58 |
| 59 <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!!" /> | 59 <inputs> |
| 60 <repeat name="rep_factorLevel" title="Factor level" min="1"> | 60 <param format="tabular" name="expression_matrix" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" /> |
| 61 <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!!" /> | 61 |
| 62 <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"> | 62 <repeat name="treatments" title="Factor/Condition" min="1"> |
| 63 <validator type="no_options" message="Please select at least one column." /> | 63 <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!!" /> |
| 64 </param> | 64 <repeat name="rep_factorLevel" title="Factor level" min="1"> |
| 65 </repeat> | 65 <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!!" /> |
| 66 </repeat> | 66 <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"> |
| 67 | 67 <validator type="no_options" message="Please select at least one column." /> |
| 68 <conditional name="choose_blocking"> | 68 </param> |
| 69 <param name="choice" type="select" label="Define blocking (paired or grouped samples)" help="e.g. to remove batch effects" > | 69 </repeat> |
| 70 <option value="false">No</option> | 70 </repeat> |
| 71 <option value="true">Yes</option> | 71 |
| 72 </param> | 72 <conditional name="choose_blocking"> |
| 73 <when value="false" /> | 73 <param name="choice" type="select" label="Define blocking (paired or grouped samples)" help="e.g. to remove batch effects" > |
| 74 <when value="true"> | 74 <option value="false">No</option> |
| 75 <repeat name="blocking_repeat" title="Blocking condition" min="1"> | 75 <option value="true">Yes</option> |
| 76 <param name="blocking_name" type="text" value="" label="Specify a name for a blocking condition" help="e.g.'Patients' or 'Batches'" /> | 76 </param> |
| 77 <repeat name="block" title="Block" min="2"> | 77 <when value="false" /> |
| 78 <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"> | 78 <when value="true"> |
| 79 <validator type="no_options" message="Please select at least one column." /> | 79 <repeat name="blocking_repeat" title="Blocking condition" min="1"> |
| 80 </param> | 80 <param name="blocking_name" type="text" value="" label="Specify a name for a blocking condition" help="e.g.'Patients' or 'Batches'" /> |
| 81 </repeat> | 81 <repeat name="block" title="Block" min="2"> |
| 82 </repeat> | 82 <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"> |
| 83 </when> | 83 <validator type="no_options" message="Please select at least one column." /> |
| 84 </conditional> | 84 </param> |
| 85 </inputs> | 85 </repeat> |
| 86 | 86 </repeat> |
| 87 <outputs> | 87 </when> |
| 88 <data format="tabular" name="design_matrix" label="Design matrix" /> | 88 </conditional> |
| 89 </outputs> | 89 </inputs> |
| 90 | 90 |
| 91 | 91 <outputs> |
| 92 <tests> | 92 <data format="tabular" name="design_matrix" label="Design matrix" /> |
| 93 <test> | 93 </outputs> |
| 94 <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" /> | 94 |
| 95 | 95 |
| 96 <!-- <repeat name="treatments"> --> | 96 <tests> |
| 97 <param name="treatments_0|name" value="Treatment" /> | 97 <test> |
| 98 <!-- <repeat name="rep_factorLevel"> --> | 98 <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" /> |
| 99 <param name="treatments_0|rep_factorLevel_0|factorLevel" value="Control" /> | 99 |
| 100 <param name="treatments_0|rep_factorLevel_0|factorIndex" value="2,3,4,5,6,7,8" /> | 100 <!-- <repeat name="treatments"> --> |
| 101 <!-- </repeat> --> | 101 <param name="treatments_0|name" value="Treatment" /> |
| 102 <!-- <repeat name="rep_factorLevel"> --> | 102 <!-- <repeat name="rep_factorLevel"> --> |
| 103 <param name="treatments_0|rep_factorLevel_1|factorLevel" value="E2" /> | 103 <param name="treatments_0|rep_factorLevel_0|factorLevel" value="Control" /> |
| 104 <param name="treatments_0|rep_factorLevel_1|factorIndex" value="9,10,11,12,13,14,15" /> | 104 <param name="treatments_0|rep_factorLevel_0|factorIndex" value="2,3,4,5,6,7,8" /> |
| 105 <!-- </repeat> --> | 105 <!-- </repeat> --> |
| 106 <!-- </repeat> --> | 106 <!-- <repeat name="rep_factorLevel"> --> |
| 107 | 107 <param name="treatments_0|rep_factorLevel_1|factorLevel" value="E2" /> |
| 108 <conditional name="choose_blocking"> | 108 <param name="treatments_0|rep_factorLevel_1|factorIndex" value="9,10,11,12,13,14,15" /> |
| 109 <param value="false" /> | 109 <!-- </repeat> --> |
| 110 </conditional> | 110 <!-- </repeat> --> |
| 111 | 111 |
| 112 <output name="design_matrix" file="GSE51403/GSE51403_design_matrix_full_depth.txt" /> | 112 <conditional name="choose_blocking"> |
| 113 </test> | 113 <param value="false" /> |
| 114 </tests> | 114 </conditional> |
| 115 | 115 |
| 116 <help> | 116 <output name="design_matrix" file="GSE51403/GSE51403_design_matrix_full_depth.txt" /> |
| 117 </test> | |
| 118 </tests> | |
| 119 | |
| 120 <help> | |
| 117 edgeR: Design- from Expression matrix | 121 edgeR: Design- from Expression matrix |
| 118 ##################################### | 122 ##################################### |
| 119 | 123 |
| 120 Overview | 124 Overview |
| 121 -------- | 125 -------- |
| 129 **References** | 133 **References** |
| 130 | 134 |
| 131 The test data is coming from: doi: 10.1093/bioinformatics/btt688. | 135 The test data is coming from: doi: 10.1093/bioinformatics/btt688. |
| 132 http://www.ncbi.nlm.nih.gov/pubmed/24319002 | 136 http://www.ncbi.nlm.nih.gov/pubmed/24319002 |
| 133 | 137 |
| 134 Contact | 138 @CONTACT@ |
| 135 ------- | 139 </help> |
| 136 | 140 |
| 137 The tool wrapper has been written by Youri Hoogstrate from the Erasmus | 141 <expand macro="citations" /> |
| 138 Medical Center (Rotterdam, Netherlands) on behalf of the Translational | |
| 139 Research IT (TraIT) project: | |
| 140 | |
| 141 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch | |
| 142 | |
| 143 More tools by the Translational Research IT (TraIT) project can be found | |
| 144 in the following toolsheds: | |
| 145 | |
| 146 http://toolshed.dtls.nl/ | |
| 147 | |
| 148 http://toolshed.g2.bx.psu.edu | |
| 149 | |
| 150 http://testtoolshed.g2.bx.psu.edu/ | |
| 151 </help> | |
| 152 | |
| 153 <citations> | |
| 154 <citation type="doi">10.1093/bioinformatics/btp616</citation> | |
| 155 <citation type="doi">10.1093/bioinformatics/btt688</citation> | |
| 156 </citations> | |
| 157 </tool> | 142 </tool> |