| Next changeset 1:3867289e6c1a (2020-04-24) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1" |
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added:
scpred_eigen_decomp.xml scpred_macros.xml |
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| diff -r 000000000000 -r c6fd7cbaf247 scpred_eigen_decomp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scpred_eigen_decomp.xml Wed Apr 08 06:25:22 2020 -0400 |
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| @@ -0,0 +1,31 @@ +<tool id="scpred_eigen_decompose" name="Scpred eigen-decompose" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Perform matrix eigen-decomposition; initialize object of scPred class</description> + <macros> + <import>scpred_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + scpred_eigen_decomp.R --training-matrix "${training_matrix}" --log-transform "${log_transform}" --training-labels "${training_labels}" --principal-comps "${principal_components}" --output-path "${output_object_path}" ]]></command> + <inputs> + <param type="data" name="training_matrix" label="Training matrix" format="rdata" help="Training matrix obtained from train/test split step" /> + <param type="boolean" name="log_transform" label="log-transform" checked="True" help="Should log-transform be performed on training data?" /> + <param type="data" name="training_labels" label="training labels file" format="txt" help="Path to training labels in text format" /> + <param type="integer" name="principal_components" label="Number of pincipal components" value="10" help="Number of principal components" /> + </inputs> + <outputs> + <data name="output_object_path" format="rdata" /> + </outputs> + <tests> + <test> + <param name="training_matrix" value="train_matrix.mtx" /> + <param name="training_labels" value="train_metadata.txt" /> + <output name="output_object_path" file="scPred_object.rds" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r c6fd7cbaf247 scpred_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scpred_macros.xml Wed Apr 08 06:25:22 2020 -0400 |
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| @@ -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> + |