Mercurial > repos > kkonganti > lexmapr2_from_cfsan

comparison cfsan_lexmapr2.xml @ 17:b4ef74a844e6

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"planemo upload"
author kkonganti
date Thu, 15 Sep 2022 14:41:43 -0400
parents 64fe14d9e2c8
children 62b848017a6a
comparison
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16:64fe14d9e2c8 17:b4ef74a844e6
34 #end if 34 #end if
35 #if $input_json.json_is_set: 35 #if $input_json.json_is_set:
36 -u "$input_json.upload" 36 -u "$input_json.upload"
37 #end if 37 #end if
38 -o lexmapr2_output.tsv 38 -o lexmapr2_output.tsv
39 ./lexmapr2-input/$input.name 39 ./lexmapr2-input/$input.name;
40 mv 'lexmapr_run.log' 'lexmapr2_run_log.txt' || exit 1;
40 ]]></command> 41 ]]></command>
41 <environment_variables> 42 <environment_variables>
42 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable> 43 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
43 <environment_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable> 44 <environment_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable>
44 </environment_variables> 45 </environment_variables>
65 label="Remove ancestral terms from output" help="Default: false"/> 66 label="Remove ancestral terms from output" help="Default: false"/>
66 </inputs> 67 </inputs>
67 <outputs> 68 <outputs>
68 <data name="lexmapr2_output" format="tsv" label="Lexmapr2: Results On ${on_string}" from_work_dir="lexmapr2_output.tsv"/> 69 <data name="lexmapr2_output" format="tsv" label="Lexmapr2: Results On ${on_string}" from_work_dir="lexmapr2_output.tsv"/>
69 <collection name="plots" type="list" label="Lexmapr2: Plots on ${on_string}"> 70 <collection name="plots" type="list" label="Lexmapr2: Plots on ${on_string}">
70 <discover_datasets ext="png" directory="lexmapr_figures"/> 71 <discover_datasets pattern="(?P&lt;designation&gt;.+)" ext="png" directory="lexmapr_figures"/>
71 </collection> 72 </collection>
72 <data name="lexmapr2_log" format="txt" label="Lexmapr2: Log On ${on_string}" from_work_dir="lexmapr_run.log"/> 73 <data name="lexmapr2_log" format="txt" label="Lexmapr2: Log On ${on_string}" from_work_dir="lexmapr2_run_log.txt"/>
73 </outputs> 74 </outputs>
74 <tests> 75 <tests>
75 <test expect_num_outputs="2"> 76 <test expect_num_outputs="2">
76 <param name="input" value="test.csv"/> 77 <param name="input" value="test.csv"/>
77 </test> 78 </test>