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comparison profrep.xml @ 6:1c25246f6e68 draft default tip

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author petr-novak
date Thu, 27 Jun 2019 09:51:41 -0400
parents e27e86406f56
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5:ad3bbf392135 6:1c25246f6e68
13 <requirement type="package">profrep</requirement> 13 <requirement type="package">profrep</requirement>
14 <requirement type="package" version="1.0">profrep_databases</requirement> 14 <requirement type="package" version="1.0">profrep_databases</requirement>
15 <requirement type="package" version="1.16.4">jbrowse</requirement> 15 <requirement type="package" version="1.16.4">jbrowse</requirement>
16 </requirements> 16 </requirements>
17 <command> 17 <command>
18 which python3 > /home/petr/tmp/profreptest/env; 18 env > /tmp/profrep_test_env;
19 19
20 #if not $custom_data.options_custom_data: 20 #if not $custom_data.options_custom_data:
21 profrep_reads=\$(awk -v var="${custom_data.prepared_dataset}" 'BEGIN{FS="\t"}{if ($1 == var) print $3}' $__tool_data_path__/profrep/prepared_datasets.txt) &amp;&amp; 21 profrep_reads=\$(awk -v var="${custom_data.prepared_dataset}" 'BEGIN{FS="\t"}{if ($1 == var) print $3}' $__tool_data_path__/profrep/prepared_datasets.txt) &amp;&amp;
22 profrep_cls=\$(awk -v var="${custom_data.prepared_dataset}" 'BEGIN{FS="\t"}{if ($1 == var) print $4}' $__tool_data_path__/profrep/prepared_datasets.txt) &amp;&amp; 22 profrep_cls=\$(awk -v var="${custom_data.prepared_dataset}" 'BEGIN{FS="\t"}{if ($1 == var) print $4}' $__tool_data_path__/profrep/prepared_datasets.txt) &amp;&amp;
23 profrep_annotation=\$(awk -v var="${custom_data.prepared_dataset}" 'BEGIN{FS="\t"}{if ($1 == var) print $5}' $__tool_data_path__/profrep/prepared_datasets.txt) &amp;&amp; 23 profrep_annotation=\$(awk -v var="${custom_data.prepared_dataset}" 'BEGIN{FS="\t"}{if ($1 == var) print $5}' $__tool_data_path__/profrep/prepared_datasets.txt) &amp;&amp;