Mercurial > repos > kkonganti > lexmapr2_from_cfsan

comparison cfsan_lexmapr2.xml @ 15:7af47af89580

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"planemo upload"
author kkonganti
date Thu, 15 Sep 2022 14:21:53 -0400
parents 89998b9b4d46
children 64fe14d9e2c8
comparison
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14:89998b9b4d46 15:7af47af89580
33 $graph 33 $graph
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 "$input_json.upload"
37 #end if 37 #end if
38 -o lexmapr2_output.tsv
38 ./lexmapr2-input/$input.name 39 ./lexmapr2-input/$input.name
39 ]]></command> 40 ]]></command>
40 <environment_variables> 41 <environment_variables>
41 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable> 42 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
42 <environment_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable> 43 <environment_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable>
56 </conditional> 57 </conditional>
57 <param name="bins" truevalue="-b" type="boolean" checked="true" 58 <param name="bins" truevalue="-b" type="boolean" checked="true"
58 label="Classify samples into default bins" help="Default: true"/> 59 label="Classify samples into default bins" help="Default: true"/>
59 <param name="graph" truevalue="-g" type="boolean" checked="true" 60 <param name="graph" truevalue="-g" type="boolean" checked="true"
60 label="Visualize summary of mapping and binning" help="Default: true"/> 61 label="Visualize summary of mapping and binning" help="Default: true"/>
61 <param name="full" truevalue="-f" type="boolean" checked="false" 62 <param name="full" truevalue="-f" type="boolean" checked="true"
62 label="Generate full output format" help="Default: false"/> 63 label="Generate full output format" help="Default: true"/>
63 <param name="no_ancestors" truevalue="-a" type="boolean" checked="false" 64 <param name="no_ancestors" truevalue="-a" type="boolean" checked="false"
64 label="Remove ancestral terms from output" help="Default: false"/> 65 label="Remove ancestral terms from output" help="Default: false"/>
65 </inputs> 66 </inputs>
66 <outputs> 67 <outputs>
67 <data name="lexmapr2_output" format="tsv" label="Lexmapr2: On ${on_string}" from_work_dir="lexmapr2_output.tsv"/> 68 <data name="lexmapr2_output" format="tsv" label="Lexmapr2: On ${on_string}" from_work_dir="lexmapr2_output.tsv"/>