diff scmap_get_std_output.xml @ 8:601a933714f1 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8350493268ce3ced12b1133b9b0f734a288deb75

--- a/scmap_get_std_output.xml	Fri Nov 27 13:42:47 2020 +0000
+++ b/scmap_get_std_output.xml	Tue Apr 23 07:49:05 2024 +0000
@@ -5,7 +5,12 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}"  --tool '${tool}' --sim-col-name "${sim_col_name}"
+        scmap_get_std_output.R
+        --predictions-file "${input_predictions_file}"
+        --output-table "${output_predictions_file}"
+        --include-scores "${include_scores}"
+        --tool '${tool}'
+        --sim-col-name "${sim_col_name}"
         #if $index
           --index "${index}"
         #end if   
@@ -21,13 +26,19 @@
         <param type="text" name="sim_col_name" value="scmap_cluster_siml" label="Column name of similarity scores" help="Name of column that contains distances between clusters/cells" />
     </inputs>
     <outputs>
-        <data name="output_predictions_file" format="txt" />
+        <data name="output_predictions_file" format="tabular" />
     </outputs>
     <tests>
         <test>
             <param name="input_predictions_file" value="closest_cells_clusters.tsv" />
             <param name="include_scores" value="TRUE" />
-            <output name="output_predictions_file" value="scmap_output_tbl.txt" compare="sim_size" />
+            <output name="output_predictions_file">
+                <assert_contents>
+                    <has_n_lines n="92"/>
+                    <has_text text="predicted_label"/>
+                    <has_text text="Zygote..3.RPKM."/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[