Mercurial > repos > mzhuang > chess_preprocessor
view chess_preprocessor.xml @ 3:4419368c8287 draft default tip
"planemo upload"
author | mzhuang |
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date | Mon, 27 Sep 2021 18:50:33 +0000 |
parents | 43a20d0e2985 |
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<tool id="chess_preprocessor" name="CHESS Preprocessing Tool" version="0.2.1"> <description>for pre-processing raw data</description> <requirements> <requirement type="package" version="0.8.4">hexrd</requirement> </requirements> <command><![CDATA[ #import os.path mkdir -p output; cd output; #if $input_source_conditional.input_source == "input_source_history" #set $input_type = $input_source_conditional.input_type_conditional.input_type #if $input_type == "single" #set $input_data = $input_source_conditional.input_type_conditional.fastq_input1 #elif $input_type == "list_collection" #set $input_data = $input_source_conditional.input_type_conditional.fastq_input #end if# #set $var = "" #for $f in $input_data# #set $var += "${f}\n" #end for# #set files = '\\n'.join([str($file) for $file in $input_data]) ##for $f in $input_data# #if $output_as_list == "Yes" ##printf "$files" >> '$output_list_log' 2>&1; printf "$files" | xargs -n 1 -P \${GALAXY_SLOTS} -I{} python '$__tool_directory__/preprocess_dexela_h5_galaxy.py' {} -o '$ome_start' -s '$start_frame' -n '$num_frames' -e '$ome_end' -t '$threshold' >> '$output_list_log' 2>&1; #elif $output_as_list == "No" printf "$files" | xargs -n 1 -P \${GALAXY_SLOTS} -I{} python '$__tool_directory__/preprocess_dexela_h5_galaxy.py' {} -o '$ome_start' -s '$start_frame' -n '$num_frames' -e '$ome_end' -t '$threshold' >> '$output' 2>&1; #end if# ##end for# #elif $input_source_conditional.input_source == "input_source_linux" #set $scans = [i for a in [(int(j[0]),int(j[-1])+1) for j in [x.split(':') for x in $input_source_conditional.scan_numbers.split(',')]] for i in range(a[0],a[1])] ##set $scanlist = '\n'.join($scans) #for $n in $scans# #if $output_as_list == "Yes" echo '$input_source_conditional.base_dir' >> '$output_list_log'; python '$__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_list_log' 2>&1; #elif $output_as_list == "No" echo '$input_source_conditional.base_dir' >> '$output'; python '__tool_directory__/preprocess_dexela_h5_filesystem.py' '$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; #end if# #end for# #end if# ]]></command> <inputs> <!-- <param name="infile_" type="data" multiple="true" label="Any file"/> --> <conditional name="input_source_conditional"> <param name="input_source" type="select" label="Location of raw data"> <option value="input_source_history" selected="true">Choose from History panel</option> <option value="input_source_linux">Specify a directory in CHESS file system </option> </param> <when value="input_source_history"> <conditional name="input_type_conditional"> <param name="input_type" type="select" label="Input raw data as"> <option value="list_collection" selected="true">List of Datasets</option> <option value="single">Dataset(s)</option> </param> <when value="single"> <param name="fastq_input1" type="data" multiple="true" label="Select (a) raw data file(s)" help="Specify (a) raw data file(s) for pre-processing"/> </when> <when value="list_collection"> <param name="fastq_input" type="data_collection" collection_type="list" label="Select a list of raw data files" help="Specify a list of raw data files for pre-processing one by one"/> </when> </conditional> </when> <when value="input_source_linux"> <param name="base_dir" type="text" label="Please specify the directory that contains raw data"> <sanitizer> <valid initial="string.ascii_letters,string.digits"> <add value="#,/,*,@,.,_,-" /> <add value="_" /> </valid> </sanitizer> </param> <param name="expt_name" type="text" label="Please specify the experiment name"/> <param name="samp_name" type="text" label="Please specify the sample name"/> <param name="scan_numbers" type="text" label="Please specify a scan number or scan numbers separated by comma (for example, 5,7,8,9,20,21,22,23,30 or 5,7:9,20:23,30)"/> </when> </conditional> <!-- <param name="which_cluster" type="select" label="Send your job to below cluster"> <option value="SDSC" selected="true">SDSC</option> <option value="Cornell" selected="true">Cornell CHESS</option> </param> --> <!-- <param name="output_dir" type="text" hidden="true"/> --> <param name="num_frames" type="integer" value="999" label="Number of frames to read"/> <param name="start_frame" type="integer" value="0" label="Index of first data frame"/> <param name="threshold" type="integer" value="50" label="Threshold for frame caches"/> <param name="ome_start" type="float" value="-50.0" label="Start omega"/> <param name="ome_end" type="float" value="49.9" label="End omega"/> <param name="output_as_list" type="select" label="Would you like the tool to output result(s) as a list?"> <option value="Yes" selected="true">Yes. Let the results be contained in a list.</option> <option value="No" >No. Show them individually.</option> </param> </inputs> <outputs> <data format="txt" name="output_list_log" label="${tool.name} on ${on_string}"> <!--filter>input_type_conditional['input_type'] == 'single'</filter--> <filter>output_as_list == 'Yes'</filter> </data> <!-- <collection name="output_list" type="list" label="${tool.name} on ${on_string}: processed_data" structured_like="fastq_input" format="npz"> <collection name="output_list" type="list" label="${tool.name} on ${on_string}: processed_data" format="npz"> --> <collection name="output_list" type="list" label="${tool.name} on ${on_string}: processed_data"> <!-- discover_datasets pattern="__name_and_ext__" directory="output" ext="npz" visible="false"/--> <discover_datasets pattern="(?P<designation>.+)\.npz" ext="hexrd.npz" directory="output"/> <!--discover_datasets pattern="(?P<designation>.+)\.npz" ext="npz" directory="output"/--> <!--discover_datasets pattern="(?P<designation>.npz)" ext="hexrd.npz" directory="output"/--> <!--filter>input_type_conditional['input_type'] == 'list_collection'</filter--> <filter>output_as_list == 'Yes'</filter> </collection> <data format="txt" name="output" label="${tool.name} on ${on_string}"> <discover_datasets pattern="(?P<designation>.+)\.npz" directory="output" ext="hexrd.npz" visible="true" /> <filter>output_as_list == 'No'</filter> </data> <!--data format="txt" name="output_list" label="${tool.name} on ${on_string}: listfiles"> <filter>input_type_conditional['input_type'] == 'list_collection'</filter> </data --> </outputs> </tool>