| Next changeset 1:148fae20fe64 (2020-04-24) |
|
Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1" |
|
added:
scpred_macros.xml scpred_train_test_split.xml |
| b |
| diff -r 000000000000 -r 8ec19f24fcf3 scpred_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scpred_macros.xml Wed Apr 08 06:37:16 2020 -0400 |
| [ |
| @@ -0,0 +1,46 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.0</token> + <token name="@HELP@">More information can be found at https://joseah.github.io/post/introduction-to-scpred/</token> + <token name="@PROFILE@">18.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.5">scpred-cli</requirement> + <yield/> + </requirements> + </xml> + <xml name="version"> + <version_command><![CDATA[ + echo $(R --version | grep version | grep -v GNU)", scpred version" $(R --vanilla --slave -e "library(scpred); cat(sessionInfo()\$otherPkgs\$scpred\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + </xml> + <token name="@VERSION_HISTORY@"><![CDATA[ + **Version history** + 1.0.0+galaxy0: Initilal contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. + ]]></token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @article{Alquicira-Hernandez2019, + author = {Alquicira-Hernandez, Jose and Sathe, Anuja and Ji, Hanlee P and Nguyen, Quan and Powell, Joseph E}, + journal = {Genome Biology}, + title = {{scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data}}, + url = {https://doi.org/10.1186/s13059-019-1862-5}, + year = {2019} + } + </citation> + <citation type="bibtex"> + @misc{githubscpred-cli.git, + author = {Andrey Solovyev, EBI Gene Expression Team}, + year = {2019}, + title = {scpred-cli: command line interface for ScPred tool}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/scpred-cli.git}, + } + + </citation> + <yield /> + </citations> + </xml> +</macros> + |
| b |
| diff -r 000000000000 -r 8ec19f24fcf3 scpred_train_test_split.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scpred_train_test_split.xml Wed Apr 08 06:37:16 2020 -0400 |
| [ |
| @@ -0,0 +1,37 @@ +<tool id="scpred_traint_test_split" name="Scpred train-test split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>CPM normalise and partition into train/test data</description> + <macros> + <import>scpred_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + scpred_train_test_split.R --input-sce-object "${input_sce_object}" --normalised-counts-slot "${norm_counts_slot}" --training-matrix "${training_mat}" --test-matrix "${test_mat}" --cell-types-column "${cell_types_col}" --training-labels "${training_labs}" --test-labels "${test_labs}" --training-ratio "${training_ratio}" ]]></command> + <inputs> + <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" /> + <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" /> + <param type="text" name="cell_types_col" label="Column name for assigned cell types" /> + <param type="float" name="training_ratio" label="Train/test split ratio" value="0.7" help="What proportion of the data set (0 to 1) should be used for training" /> + </inputs> + <outputs> + <data name="training_mat" format="rdata" /> + <data name="test_mat" format="rdata" /> + <data name="training_labs" format="txt" /> + <data name="test_labs" format="txt" /> + </outputs> + <tests> + <test> + <param name="input_sce_object" value="pollen_cpm.rds" /> + <param name="cell_types_col" value="cell_type2" /> + <output name="training_mat" file="train_matrix.mtx" compare="sim_size"/> + <output name="test_mat" file="test_matrix.mtx" compare="sim_size"/> + <output name="training_labs" file="train_metadata.txt" compare="sim_size" /> + <output name="test_labs" file="test_metadata.txt" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool> |