diff pysradb.xml @ 2:b91e1e70f3a1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb commit 2d911e00c68a1be27d3627acd5020ee12378919b

--- a/pysradb.xml	Wed Nov 30 13:19:36 2022 +0000
+++ b/pysradb.xml	Mon Jan 23 16:10:06 2023 +0000
@@ -13,9 +13,7 @@
     #else
         --query '${query}'
     #end if
-    #if $conditional_mode.source
-        --source '${conditional_mode.source}'
-    #end if
+    --source '${conditional_mode.source}'
     #if $conditional_mode.selector == 'false'
         --organism '${conditional_mode.organism}'
     #end if
@@ -28,7 +26,6 @@
     #if $selection
         --selection '${selection}'
     #end if
-    --source $conditional_mode.source
     #if $strategy
         --strategy '${strategy}'
     #end if
@@ -62,7 +59,7 @@
                 &&  gawk -F '\t' '{print $12}' 'output.tsv' | tail -n +2 | sort | uniq -c | gawk '{ print "    ", $0 }' >> stats.txt
             #end if
         #end if
-        && echo $'\n  Query keyworkds: ${query}\n'  >> stats.txt
+        && echo $'\n  Query keywords: ${query}\n'  >> stats.txt
     #end if
     #if 'graphs' in $output_options.output_files
         && convert 'search_plots/Histogram*.svg' -set filename:fn '%[basename]' 'search_plots/%[filename:fn].jpg'
@@ -288,12 +285,34 @@
                     <param name="max" value="100"/>
                     <param name="output_files" value="stats,graphs"/>
                 </section>
-                <output name="metadata_file" file="test_01.tabular" ftype="tsv"/>
-                <output name="stats" file="test_01_stats.txt" ftype="txt"/>
+                <output name="metadata_file" ftype="tsv">
+                    <assert_contents>
+                        <has_n_lines n="101"/>
+                        <has_n_columns n="16"/>
+                    </assert_contents>
+                </output>
+                <output name="stats" ftype="txt">
+                    <assert_contents>
+                        <has_text text="Statistics for the search query:"/>
+                        <has_text text="Query keywords: cancer"/>
+                    </assert_contents>
+                </output>
                 <output_collection name="graphs_collection" type="list" count="3">
-                    <element name="histogram_base_count" file="test_01_histogram1.jpg" ftype="jpg" compare='sim_size'/>
-                    <element name="histogram_library" file="test_01_histogram2.jpg" ftype="jpg" compare='sim_size'/>
-                    <element name="histogram_publication" file="test_01_histogram3.jpg" ftype="jpg" compare='sim_size'/>
+                    <element name="histogram_base_count" ftype="jpg">
+                        <assert_contents>
+                            <has_size value="82507" delta="10000"/>
+                        </assert_contents>
+                    </element>
+                    <element name="histogram_library" ftype="jpg">
+                        <assert_contents>
+                            <has_size value="49925" delta="10000"/>
+                        </assert_contents>
+                    </element>
+                    <element name="histogram_publication" ftype="jpg">
+                        <assert_contents>
+                            <has_size value="46059" delta="10000"/>
+                        </assert_contents>
+                    </element>
                 </output_collection>
             </test>
             <!-- Test 02: Specific search options-->