Mercurial > repos > mzhuang > chess_preprocessor
comparison chess_preprocessor.xml @ 3:4419368c8287 draft default tip
"planemo upload"
author | mzhuang |
---|---|
date | Mon, 27 Sep 2021 18:50:33 +0000 |
parents | 43a20d0e2985 |
children |
comparison
equal
deleted
inserted
replaced
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 --> |