Mercurial > repos > ebi-gxa > update_marker_file

changeset 1:5036928f60bc draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
author ebi-gxa
date Fri, 24 Apr 2020 11:23:13 -0400
parents 8ee96cde3643
children 3a1cfbb8aa56
files garnett_macros.xml update_marker_file.xml
diffstat 2 files changed, 14 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/garnett_macros.xml	Wed Apr 08 06:32:25 2020 -0400
+++ b/garnett_macros.xml	Fri Apr 24 11:23:13 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>
-
--- a/update_marker_file.xml	Wed Apr 08 06:32:25 2020 -0400
+++ b/update_marker_file.xml	Fri Apr 24 11:23:13 2020 -0400
@@ -5,7 +5,17 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}' --summary-col '${summary_col}' --cell-type-col '${cell_type_col}' --gene-id-col '${gene_id_col}' --updated-marker-file '${updated_marker_file}' 
+        update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}'    --updated-marker-file '${updated_marker_file}'
+
+        #if $summary_col
+        --summary-col '${summary_col}'
+        #end if
+        #if $cell_type_col
+        --cell-type-col '${cell_type_col}'
+        #end if
+        #if $gene_id_col
+        --gene-id-col '${gene_id_col}'
+        #end if
     ]]></command>
     <inputs>
         <param type="data" name="marker_list_obj" label="Marker list object" format="rdata" help="Serialised object containing markers list produced by garnett_transform_markers" />