Mercurial > repos > ebi-gxa > ct_build_cell_ontology_dict

changeset 1:7086be9e707e 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 11:20:33 -0400
parents 406d293e567e
children f1f720a9b679
files ct_build_cell_ontology_dict.xml ct_macros.xml
diffstat 2 files changed, 16 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/ct_build_cell_ontology_dict.xml	Wed Apr 08 11:35:35 2020 -0400
+++ b/ct_build_cell_ontology_dict.xml	Fri Apr 24 11:20:33 2020 -0400
@@ -10,7 +10,20 @@
             cp '$sdrf' input_dir/;
         #end for
 
-        build_cell_ontology_dict.R --input-dir input_dir --condensed-sdrf "${condensed_sdrf}" --barcode-col-name "${barcode_col_name}" --cell-label-col-name "${cell_label_col_name}" --cell-ontology-col-name "${cell_ontology_col_name}" --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}" ]]></command>
+        build_cell_ontology_dict.R --input-dir input_dir  --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}"
+        #if $condensed_sdrf
+        --condensed-sdrf "${condensed_sdrf}" 
+        #end if
+        #if $barcode_col_name
+        --barcode-col-name "${barcode_col_name}"
+        #end if
+        #if $cell_label_col_name
+        --cell-label-col-name "${cell_label_col_name}"
+        #end if
+        #if $cell_ontology_col_name
+        --cell-ontology-col-name "${cell_ontology_col_name}" 
+        #end if
+         ]]></command>
     <inputs>
         <param type="data" name="input_sdrfs" label="Input SDRF tables" multiple="true" format="tsv" help="Input SDRF tables" />
         <param type="boolean" name="condensed_sdrf" checked="false" label="Condensed SDRF" help="Are the supplied SDRFs of condensed format?" />
--- a/ct_macros.xml	Wed Apr 08 11:35:35 2020 -0400
+++ b/ct_macros.xml	Fri Apr 24 11:20:33 2020 -0400
@@ -29,7 +29,8 @@
             url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git},
           }
         </citation>
+        <citation type="doi">10.1101/2020.04.08.032698</citation>
         <yield />
       </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>