Mercurial > repos > kkonganti > lexmapr2_from_cfsan

comparison cfsan_lexmapr2.xml @ 8:f4c56a885fdc

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"planemo upload"
author kkonganti
date Thu, 15 Sep 2022 13:38:06 -0400
parents 1a016f646687
children 9c2c4e53beb8
comparison
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7:1a016f646687 8:f4c56a885fdc
11 <requirement type="package">seaborn</requirement> 11 <requirement type="package">seaborn</requirement>
12 <requirement type="package">pygraphviz</requirement> 12 <requirement type="package">pygraphviz</requirement>
13 </requirements> 13 </requirements>
14 <version_command>python $__tool_directory__/lexmapr2.py --version</version_command> 14 <version_command>python $__tool_directory__/lexmapr2.py --version</version_command>
15 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
16 export PYTHON_PATH=
16 mkdir -p lexmapr2-input || exit 1; 17 mkdir -p lexmapr2-input || exit 1;
17 ln -sf '$input' './lexmapr2-input/$input.name'; 18 ln -sf '$input' './lexmapr2-input/$input.name';
18 python $__tool_directory__/lexmapr2.py 19 python $__tool_directory__/lexmapr2.py
19 #if ($embl_ont != ""): 20 #if ($embl_ont != ""):
20 -e $embl_ont 21 -e $embl_ont
36 #end if 37 #end if
37 ./lexmapr2-input/$input.name 38 ./lexmapr2-input/$input.name
38 ]]></command> 39 ]]></command>
39 <environment_variables> 40 <environment_variables>
40 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable> 41 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
41 <environment_variable name="PYTHON_PATH">if [ ! -z "\$PYTHON_PATH" ]; then echo "/tool/tool-data/cfsan_lexmapr2/0:\$PYTHON_PATH"; else echo "\$PYTHON_PATH"; fi</environment_variable> 42 <environment_variable name="PYTHONPATH">if [ ! -z "\$PYTHONPATH" ]; then echo "/tool/tool-data/cfsan_lexmapr2/0:\$PYTHONPATH"; else echo "\$PYTHONPATH"; fi</environment_variable>
42 </environment_variables> 43 </environment_variables>
43 <inputs> 44 <inputs>
44 <param name="input" type="data" format="csv" label="Input CSV" 45 <param name="input" type="data" format="csv" label="Input CSV"
45 help="First row should be a header and first column should be sample names" /> 46 help="First row should be a header and first column should be sample names" />
46 <param name="embl_ont" type="text" optional="true" 47 <param name="embl_ont" type="text" optional="true"