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"planemo upload"
author mzhuang
date Mon, 27 Sep 2021 18:50:33 +0000
parents 43a20d0e2985
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2:43a20d0e2985 3:4419368c8287
1 <tool id="chess_preprocessor" name="CHESS Preprocessing Tool" version="0.2.0"> 1 <tool id="chess_preprocessor" name="CHESS Preprocessing Tool" version="0.2.1">
2 <description>for pre-processing raw data</description> 2 <description>for pre-processing raw data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.8.4">hexrd</requirement> 4 <requirement type="package" version="0.8.4">hexrd</requirement>
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <command><![CDATA[
7 #import os.path 7 #import os.path
8 8
9 ##source ~/.bashrc;conda activate pulsar;
10 ##source ~/.bashrc; conda activate __hexrd@0.8.0;
11 mkdir -p output; 9 mkdir -p output;
12 cd output; 10 cd output;
13 ##set $history_id=$__app__.security.encode_id($output.creating_job.history.id)
14 ##echo '$history_id' >> '$output';
15 echo 'Hello World!' >> '$output';
16 11
17 #if $input_source_conditional.input_source == "input_source_history" 12 #if $input_source_conditional.input_source == "input_source_history"
18 #set $input_type = $input_source_conditional.input_type_conditional.input_type 13 #set $input_type = $input_source_conditional.input_type_conditional.input_type
19 #if $input_type == "single" 14 #if $input_type == "single"
20 #set $input_data = $input_source_conditional.input_type_conditional.fastq_input1 15 #set $input_data = $input_source_conditional.input_type_conditional.fastq_input1
47 echo '$input_source_conditional.base_dir' >> '$output'; 42 echo '$input_source_conditional.base_dir' >> '$output';
48 python '__tool_directory__/preprocess_dexela_h5_filesystem.py' '$input_source_conditional.base_dir' '$input_source_conditional.expt_name' '$input_source_conditional.samp_name' '$n' -o '$ome_start' -s '$start_frame' -n '$num_frames' -e '$ome_end' -t '$threshold' >> '$output' 2>&1; 43 python '__tool_directory__/preprocess_dexela_h5_filesystem.py' '$input_source_conditional.base_dir' '$input_source_conditional.expt_name' '$input_source_conditional.samp_name' '$n' -o '$ome_start' -s '$start_frame' -n '$num_frames' -e '$ome_end' -t '$threshold' >> '$output' 2>&1;
49 #end if# 44 #end if#
50 #end for# 45 #end for#
51 #end if# 46 #end if#
52 conda deactivate
53 ]]></command> 47 ]]></command>
54 <inputs> 48 <inputs>
55 <!-- 49 <!--
56 <param name="infile_" type="data" multiple="true" label="Any file"/> 50 <param name="infile_" type="data" multiple="true" label="Any file"/>
57 --> 51 -->