Mercurial > repos > iuc > pysradb_search
diff pysradb.xml @ 2:b91e1e70f3a1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb commit 2d911e00c68a1be27d3627acd5020ee12378919b
author | iuc |
---|---|
date | Mon, 23 Jan 2023 16:10:06 +0000 |
parents | f63cf0adfd87 |
children |
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--- 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-->