Mercurial > repos > ebi-gxa > sc3_calc_consens
comparison sc3-calc-consens.xml @ 0:aa83350751f5 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 11:29:09 -0400 |
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| -1:000000000000 | 0:aa83350751f5 |
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| 1 <?xml version="1.0" encoding="utf-8"?> | |
| 2 <tool id="sc3_calc_consens" name="SC3 Calculate Consensus" version="@TOOL_VERSION@+galaxy0"> | |
| 3 <description>from multiple runs of k-means clustering</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-consens.R -i '${sc3_kmeans}' -t '${clusters}' -o '${sc3_consensus}' | |
| 10 ]]></command> | |
| 11 | |
| 12 <inputs> | |
| 13 <param name="sc3_kmeans" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with stored kmeans clustering"/> | |
| 14 </inputs> | |
| 15 | |
| 16 <outputs> | |
| 17 <data name="clusters" format="csv" label="${tool.name} on ${on_string}: text table storing consensus clustering"/> | |
| 18 <data name="sc3_consensus" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment with consensus matrix."/> | |
| 19 </outputs> | |
| 20 | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="sc3_kmeans" value="sc3_kmeans.rds"/> | |
| 24 <output name="clusters" value="consensus_clusters.txt"/> | |
| 25 <output name="sc3_consensus" file="sc3_consensus.rds"/> | |
| 26 </test> | |
| 27 </tests> | |
| 28 | |
| 29 <help><![CDATA[ | |
| 30 ============================================== | |
| 31 This function calculates consensus clustering. | |
| 32 ============================================== | |
| 33 | |
| 34 Calculate consensus matrices based on the clustering solutions contained in the | |
| 35 kmeans item of the sc3 slot of the metadata(object). It then creates and | |
| 36 populates the consensus item of the sc3 slot with consensus matrices, their | |
| 37 hierarchical clusterings in hclust objects, and Silhouette indeces of the | |
| 38 clusters. It also removes the previously calculated kmeans clusterings from the | |
| 39 sc3 slot, as they are not needed for further analysis. | |
| 40 | |
| 41 @HELP@ | |
| 42 | |
| 43 @VERSION_HISTORY@ | |
| 44 ]]></help> | |
| 45 <expand macro="citations"/> | |
| 46 </tool> |