Mercurial > repos > kkonganti > lexmapr2_from_cfsan

comparison cfsan_lexmapr2.xml @ 11:abb0fc18a85d

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"planemo upload"
author kkonganti
date Thu, 15 Sep 2022 13:53:29 -0400
parents af76096f7a10
children 530cafac56f9
comparison
equal deleted inserted replaced
10:af76096f7a10 11:abb0fc18a85d
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 echo $PYTHONPATH; 16 echo $PYTHONPATH 1>&2;
17 mkdir -p lexmapr2-input || exit 1; 17 mkdir -p lexmapr2-input || exit 1;
18 ln -sf '$input' './lexmapr2-input/$input.name'; 18 ln -sf '$input' './lexmapr2-input/$input.name';
19 python $__tool_directory__/lexmapr2.py 19 python $__tool_directory__/lexmapr2.py
20 #if ($embl_ont != ""): 20 #if ($embl_ont != ""):
21 -e $embl_ont 21 -e $embl_ont
37 #end if 37 #end if
38 ./lexmapr2-input/$input.name 38 ./lexmapr2-input/$input.name
39 ]]></command> 39 ]]></command>
40 <environment_variables> 40 <environment_variables>
41 <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>
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_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable>
43 </environment_variables> 43 </environment_variables>
44 <inputs> 44 <inputs>
45 <param name="input" type="data" format="csv" label="Input CSV" 45 <param name="input" type="data" format="csv" label="Input CSV"
46 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" />
47 <param name="embl_ont" type="text" optional="true" 47 <param name="embl_ont" type="text" optional="true"