# HG changeset patch
# User ebi-gxa
# Date 1587741760 14400
# Node ID 2067ebe66b55a62ed17de8aca9b40bbef3e5ec3d
# Parent  24a22971dd44f960aac2268532b50f7e6d53341c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r 24a22971dd44 -r 2067ebe66b55 garnett_macros.xml
--- a/garnett_macros.xml	Wed Apr 08 06:28:28 2020 -0400
+++ b/garnett_macros.xml	Fri Apr 24 11:22:40 2020 -0400
@@ -4,7 +4,7 @@
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.0.3">garnett-cli</requirement>
+            <requirement type="package" version="0.0.5">garnett-cli</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -21,7 +21,7 @@
         <citations>
             <citation type="bibtex">
                 @article{,
-                url = {https://doi.org/10.1038/s41592-019-0535-3},           
+                url = {https://doi.org/10.1038/s41592-019-0535-3},
                 author = {Hannah A. Pliner and Jay Shendure and Cole Trapnell},
                 title = {Supervised classification enables rapid annotation of cell atlases},
                 journal = {Nature Methods}
@@ -38,7 +38,7 @@
                   }
             </citation>
             <yield />
+            <citation type="doi">10.1101/2020.04.08.032698</citation>
         </citations>
     </xml>
 </macros>
-
diff -r 24a22971dd44 -r 2067ebe66b55 garnett_train_classifier.xml
--- a/garnett_train_classifier.xml	Wed Apr 08 06:28:28 2020 -0400
+++ b/garnett_train_classifier.xml	Fri Apr 24 11:22:40 2020 -0400
@@ -5,12 +5,37 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        garnett_train_classifier.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --cds-gene-id-type '${cds_gene_id_type}' --marker-file-gene-id-type '${marker_file_gene_id_type}' --num-unknown '${num_unknown}' --min-observations '${min_observations}' --max-training-samples '${max_training_samples}' --propogate-markers '${propogate_markers}' --cores '${cores}' --classifier-gene-id-type '${classifier_gene_id_type}' --output-path '${output_classifier_path}'
+        garnett_train_classifier.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --cores \${GALAXY_SLOTS:-1} --output-path '${output_classifier_path}'
+        #if $train_id
+        --train-id '${train_id}' 
+        #end if
+        #if $cds_gene_id_type
+        --cds-gene-id-type '${cds_gene_id_type}' 
+        #end if
+        #if $marker_file_gene_id_type
+        --marker-file-gene-id-type '${marker_file_gene_id_type}' 
+        #end if
+        #if $num_unknown
+        --num-unknown '${num_unknown}' 
+        #end if
+        #if $min_observations
+        --min-observations '${min_observations}' 
+        #end if
+        #if $max_training_samples
+        --max-training-samples '${max_training_samples}' 
+        #end if
+        #if $propogate_markers
+        --propogate-markers '${propogate_markers}'
+        #end if
+        #if $classifier_gene_id_type
+        --classifier-gene-id-type '${classifier_gene_id_type}' 
+        #end if
     ]]></command>
     <inputs>
         <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" />
         <param type="data" name="marker_file_path" format="txt" label="Marker file path" help="File with marker genes specifying cell types. 
         See https://cole-trapnell-lab.github.io/garnett/docs/#constructing-a-marker-file for specification of the file format" />
+        <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
         <param type="text" name="database" label="gene database" value="org.Hs.eg.db" help="argument for Bioconductor AnnotationDb-class package used for converting gene IDs" />
         <param type="text" name="cds_gene_id_type" label="CDS gene id type" value="ENSEMBL" help="Format of the gene IDs in your CDS object" />
         <param type="text" name="marker_file_gene_id_type" label="Marker gene id type" value="ENSEMBL" help="Format of the gene IDs in your marker file" />
@@ -22,7 +47,6 @@
         increases speed, but may hurt performance of the model." />
         <param type="boolean" name="propogate_markers" checked="true" label="propogate markers" help="Should markers from child nodes of a cell type be used
         in finding representatives of the parent type?" />
-        <param type="integer" name="cores" label="cores" value="1" help="The number of cores to use for computation" />
         <param type="text" name="classifier_gene_id_type"  label="Classifier gene ID type" value="ENSEMBL" help="The type of gene ID that will be used in the classifier. If possible for your organism, this should be 'ENSEMBL', which is the default." />
     </inputs>
     <outputs>
@@ -41,6 +65,4 @@
         @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
-</tool>
-
-
+</tool>
\ No newline at end of file