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comparison pysradb.xml @ 2:b91e1e70f3a1 draft default tip

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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
comparison
equal deleted inserted replaced
1:f63cf0adfd87 2:b91e1e70f3a1
11 #if $conditional_platform.instrument 11 #if $conditional_platform.instrument
12 --query '${conditional_platform.instrument} ${query}' 12 --query '${conditional_platform.instrument} ${query}'
13 #else 13 #else
14 --query '${query}' 14 --query '${query}'
15 #end if 15 #end if
16 #if $conditional_mode.source 16 --source '${conditional_mode.source}'
17 --source '${conditional_mode.source}'
18 #end if
19 #if $conditional_mode.selector == 'false' 17 #if $conditional_mode.selector == 'false'
20 --organism '${conditional_mode.organism}' 18 --organism '${conditional_mode.organism}'
21 #end if 19 #end if
22 #if $conditional_platform.platform == 'illumina' 20 #if $conditional_platform.platform == 'illumina'
23 #if $conditional_platform.layout 21 #if $conditional_platform.layout
26 #end if 24 #end if
27 --platform '$conditional_platform.platform' 25 --platform '$conditional_platform.platform'
28 #if $selection 26 #if $selection
29 --selection '${selection}' 27 --selection '${selection}'
30 #end if 28 #end if
31 --source $conditional_mode.source
32 #if $strategy 29 #if $strategy
33 --strategy '${strategy}' 30 --strategy '${strategy}'
34 #end if 31 #end if
35 32
36 ## Optional fields 33 ## Optional fields
60 && gawk -F '\t' '{print $11}' 'output.tsv' | tail -n +2 | sort | uniq -c | gawk '{ print " ", $0 }' >> stats.txt 57 && gawk -F '\t' '{print $11}' 'output.tsv' | tail -n +2 | sort | uniq -c | gawk '{ print " ", $0 }' >> stats.txt
61 #else 58 #else
62 && gawk -F '\t' '{print $12}' 'output.tsv' | tail -n +2 | sort | uniq -c | gawk '{ print " ", $0 }' >> stats.txt 59 && gawk -F '\t' '{print $12}' 'output.tsv' | tail -n +2 | sort | uniq -c | gawk '{ print " ", $0 }' >> stats.txt
63 #end if 60 #end if
64 #end if 61 #end if
65 && echo $'\n Query keyworkds: ${query}\n' >> stats.txt 62 && echo $'\n Query keywords: ${query}\n' >> stats.txt
66 #end if 63 #end if
67 #if 'graphs' in $output_options.output_files 64 #if 'graphs' in $output_options.output_files
68 && convert 'search_plots/Histogram*.svg' -set filename:fn '%[basename]' 'search_plots/%[filename:fn].jpg' 65 && convert 'search_plots/Histogram*.svg' -set filename:fn '%[basename]' 'search_plots/%[filename:fn].jpg'
69 && mv 'search_plots/Histogram of Base Count'*.jpg 'search_plots/histogram_base_count.jpg' 66 && mv 'search_plots/Histogram of Base Count'*.jpg 'search_plots/histogram_base_count.jpg'
70 && mv 'search_plots/Histogram of Library'*jpg 'search_plots/histogram_library.jpg' 67 && mv 'search_plots/Histogram of Library'*jpg 'search_plots/histogram_library.jpg'
286 </conditional> 283 </conditional>
287 <section name="output_options"> 284 <section name="output_options">
288 <param name="max" value="100"/> 285 <param name="max" value="100"/>
289 <param name="output_files" value="stats,graphs"/> 286 <param name="output_files" value="stats,graphs"/>
290 </section> 287 </section>
291 <output name="metadata_file" file="test_01.tabular" ftype="tsv"/> 288 <output name="metadata_file" ftype="tsv">
292 <output name="stats" file="test_01_stats.txt" ftype="txt"/> 289 <assert_contents>
290 <has_n_lines n="101"/>
291 <has_n_columns n="16"/>
292 </assert_contents>
293 </output>
294 <output name="stats" ftype="txt">
295 <assert_contents>
296 <has_text text="Statistics for the search query:"/>
297 <has_text text="Query keywords: cancer"/>
298 </assert_contents>
299 </output>
293 <output_collection name="graphs_collection" type="list" count="3"> 300 <output_collection name="graphs_collection" type="list" count="3">
294 <element name="histogram_base_count" file="test_01_histogram1.jpg" ftype="jpg" compare='sim_size'/> 301 <element name="histogram_base_count" ftype="jpg">
295 <element name="histogram_library" file="test_01_histogram2.jpg" ftype="jpg" compare='sim_size'/> 302 <assert_contents>
296 <element name="histogram_publication" file="test_01_histogram3.jpg" ftype="jpg" compare='sim_size'/> 303 <has_size value="82507" delta="10000"/>
304 </assert_contents>
305 </element>
306 <element name="histogram_library" ftype="jpg">
307 <assert_contents>
308 <has_size value="49925" delta="10000"/>
309 </assert_contents>
310 </element>
311 <element name="histogram_publication" ftype="jpg">
312 <assert_contents>
313 <has_size value="46059" delta="10000"/>
314 </assert_contents>
315 </element>
297 </output_collection> 316 </output_collection>
298 </test> 317 </test>
299 <!-- Test 02: Specific search options--> 318 <!-- Test 02: Specific search options-->
300 <test expect_num_outputs="2"> 319 <test expect_num_outputs="2">
301 <param name="database" value="sra"/> 320 <param name="database" value="sra"/>