Mercurial > repos > devteam > cummerbund
comparison cummeRbund_macros.xml @ 0:587c425b4e76 draft
Initial commit with version 1.0.0 of the cummeRbund wrapper.
| author | devteam |
|---|---|
| date | Tue, 23 Dec 2014 15:58:27 -0500 |
| parents | |
| children | 78fcfc04fcfe |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:587c425b4e76 |
|---|---|
| 1 <?xml version="1.0"?> | |
| 2 <macros> | |
| 3 <macro name="stdio"> | |
| 4 <stdio> | |
| 5 <exit_code range="1:" /> | |
| 6 <exit_code range=":-1" /> | |
| 7 <regex match="Error:" /> | |
| 8 <regex match="Exception:" /> | |
| 9 </stdio> | |
| 10 </macro> | |
| 11 <macro name="replicates_checkbox"> | |
| 12 <param name="replicates" type="boolean" truevalue="--replicates" falsevalue="" checked="True" label="Replicates?"/> | |
| 13 </macro> | |
| 14 <macro name="log10_checkbox"> | |
| 15 <param name="log10" type="boolean" truevalue="--log10" falsevalue="" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 16 </macro> | |
| 17 <macro name="xy_selector"> | |
| 18 <param name="x" type="select" label="Sample name for x axis" dynamic_options="get_samples(input_database.dataset.file_name)" /> | |
| 19 <param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.dataset.file_name)" /> | |
| 20 </macro> | |
| 21 <macro name="genes_selector"> | |
| 22 <repeat name="genes" title="Genes"> | |
| 23 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" /> | |
| 24 </repeat> | |
| 25 </macro> | |
| 26 <macro name="features_selector"> | |
| 27 <param name="features" type="select" label="Expression levels to plot?"> | |
| 28 <option value="gene" selected="true">Genes</option> | |
| 29 <option value="isoforms">Isoforms</option> | |
| 30 <option value="tss">TSS</option> | |
| 31 <option value="cds">CDS</option> | |
| 32 </param> | |
| 33 </macro> | |
| 34 <macro name="multiple_genes_conditional"> | |
| 35 <conditional name="multiple_genes"> | |
| 36 <param name="multiple_genes_selector" type="select" label="Limit plot to genes"> | |
| 37 <option value="no" selected="true">Do not limit</option> | |
| 38 <option value="yes">Select genes</option> | |
| 39 </param> | |
| 40 <when value="yes"> | |
| 41 <expand macro="features_selector" /> | |
| 42 <expand macro="genes_selector" /> | |
| 43 </when> | |
| 44 <when value="no" /> | |
| 45 </conditional> | |
| 46 </macro> | |
| 47 </macros> |