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 |
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| 2:43a20d0e2985 | 3:4419368c8287 |
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| 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 --> |