Mercurial > repos > mzhuang > chess_test
changeset 0:c5d6fd378400 draft
"planemo upload"
| author | mzhuang |
|---|---|
| date | Sat, 25 Sep 2021 19:28:28 +0000 |
| parents | |
| children | fdc832c0cde8 |
| files | chess_test.xml |
| diffstat | 1 files changed, 95 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chess_test.xml Sat Sep 25 19:28:28 2021 +0000 @@ -0,0 +1,95 @@ +<tool id="chess_test" name="CHESS Pre-processing Tool" version="0.1.0"> + <description>for pre-processing raw data</description> + <requirements> + <requirement type="package" version="0.8.4">hexrd</requirement> + </requirements> + <command><![CDATA[ + mkdir -p output; + cd output; + set $history_id=$__app__.security.encode_id($output.creating_job.history.id) + echo '$history_id' >> '$output'; + + ]]></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> +