Mercurial > repos > ebi-gxa > sc3_calc_transfs
comparison sc3-calc-transfs.xml @ 0:b06019da7b5a draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
| author | ebi-gxa |
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| date | Wed, 03 Apr 2019 11:34:00 -0400 |
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| -1:000000000000 | 0:b06019da7b5a |
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| 1 <?xml version="1.0" encoding="utf-8"?> | |
| 2 <tool id="sc3_calc_transfs" name="SC3 Calculate Transformations" version="@TOOL_VERSION@+galaxy0"> | |
| 3 <description>of distances using PCA and graph Laplacian</description> | |
| 4 <macros> | |
| 5 <import>sc3-macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 sc3-sc3-calc-transfs.R -i '${sc3_distances}' -o '${sc3_transformed}' | |
| 10 ]]></command> | |
| 11 | |
| 12 <inputs> | |
| 13 <param name="sc3_distances" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with distances calculated"/> | |
| 14 </inputs> | |
| 15 | |
| 16 <outputs> | |
| 17 <data name="sc3_transformed" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment object with transformed distances"/> | |
| 18 </outputs> | |
| 19 | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="sc3_distances" value="sc3_distances.rdata"/> | |
| 23 <output name="sc3_transformed" file="sc3_transformed.rdata"/> | |
| 24 </test> | |
| 25 </tests> | |
| 26 | |
| 27 <help><![CDATA[ | |
| 28 ============================================== | |
| 29 This function calculate transformed distances. | |
| 30 ============================================== | |
| 31 | |
| 32 All items of the sc3 slot of the metadata(object) are transformed using either | |
| 33 principal component analysis (PCA) or by calculating the eigenvectors of the | |
| 34 associated graph Laplacian. The columns of the resulting matrices are then | |
| 35 sorted in descending order by their corresponding eigenvalues. The first d | |
| 36 columns (where d = max(metadata(object)$sc3$n_dim)) of each transformation are | |
| 37 then written to the transformations item of the sc3 slot. Additionally, this | |
| 38 function also removes the previously calculated distances from the sc3 slot, as | |
| 39 they are not needed for further analysis. | |
| 40 | |
| 41 @HELP@ | |
| 42 | |
| 43 @VERSION_HISTORY@ | |
| 44 ]]></help> | |
| 45 <expand macro="citations" /> | |
| 46 </tool> |