changeset 1:c00e672eadbc draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

--- a/garnett_check_markers.xml	Wed Apr 08 06:17:49 2020 -0400
+++ b/garnett_check_markers.xml	Fri Apr 24 11:21:22 2020 -0400
@@ -5,7 +5,23 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        garnett_check_markers.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 '${marker_file_gene_id_type}' --marker-output-path '${marker_output_path}' --plot-output-path '${plot_output_path}' --propogate-markers '${propogate_markers}' --classifier-gene-id-type '${classifier_gene_id_type}'
+        garnett_check_markers.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --marker-output-path '${marker_output_path}'
+
+        #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 $plot_output_path
+        --plot-output-path '${plot_output_path}' 
+        #end if
+        #if $propogate_markers
+        --propogate-markers '${propogate_markers}'  
+        #end if
+        #if $propogate_markers
+        --classifier-gene-id-type '${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" />

--- a/garnett_macros.xml	Wed Apr 08 06:17:49 2020 -0400
+++ b/garnett_macros.xml	Fri Apr 24 11:21:22 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>
-