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1
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1 <tool id="chess_test" name="CHESS Test Pre-processing Tool" version="0.2.0">
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0
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2 <description>for pre-processing raw data</description>
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3 <requirements>
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4 <requirement type="package" version="0.8.4">hexrd</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 mkdir -p output;
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8 cd output;
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2
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9 ##set $history_id=$__app__.security.encode_id($output.creating_job.history.id)
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10 #set $history_id='abcdefg';
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0
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11 echo '$history_id' >> '$output';
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12
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13 ]]></command>
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14 <inputs>
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15 <!--
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16 <param name="infile_" type="data" multiple="true" label="Any file"/>
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17 -->
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18 <conditional name="input_source_conditional">
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19 <param name="input_source" type="select" label="Location of raw data">
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20 <option value="input_source_history" selected="true">Choose from History panel</option>
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21 <option value="input_source_linux">Specify a directory in CHESS file system </option>
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22 </param>
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23 <when value="input_source_history">
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24 <conditional name="input_type_conditional">
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25 <param name="input_type" type="select" label="Input raw data as">
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26 <option value="list_collection" selected="true">List of Datasets</option>
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27 <option value="single">Dataset(s)</option>
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28 </param>
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29 <when value="single">
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30 <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"/>
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31 </when>
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32 <when value="list_collection">
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33 <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"/>
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34 </when>
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35 </conditional>
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36 </when>
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37 <when value="input_source_linux">
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38 <param name="base_dir" type="text" label="Please specify the directory that contains raw data">
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39 <sanitizer>
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40 <valid initial="string.ascii_letters,string.digits">
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41 <add value="#,/,*,@,.,_,-" />
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42 <add value="_" />
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43 </valid>
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44 </sanitizer>
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45 </param>
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46 <param name="expt_name" type="text" label="Please specify the experiment name"/>
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47 <param name="samp_name" type="text" label="Please specify the sample name"/>
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48 <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)"/>
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49 </when>
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50 </conditional>
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51 <!--
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52 <param name="which_cluster" type="select" label="Send your job to below cluster">
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53 <option value="SDSC" selected="true">SDSC</option>
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54 <option value="Cornell" selected="true">Cornell CHESS</option>
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55 </param>
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56 -->
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57 <!--
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58 <param name="output_dir" type="text" hidden="true"/>
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59 -->
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60 <param name="num_frames" type="integer" value="999" label="Number of frames to read"/>
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61 <param name="start_frame" type="integer" value="0" label="Index of first data frame"/>
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62 <param name="threshold" type="integer" value="50" label="Threshold for frame caches"/>
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63 <param name="ome_start" type="float" value="-50.0" label="Start omega"/>
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64 <param name="ome_end" type="float" value="49.9" label="End omega"/>
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65 <param name="output_as_list" type="select" label="Would you like the tool to output result(s) as a list?">
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66 <option value="Yes" selected="true">Yes. Let the results be contained in a list.</option>
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67 <option value="No" >No. Show them individually.</option>
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68 </param>
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69 </inputs>
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70 <outputs>
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71 <data format="txt" name="output_list_log" label="${tool.name} on ${on_string}">
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72 <!--filter>input_type_conditional['input_type'] == 'single'</filter-->
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73 <filter>output_as_list == 'Yes'</filter>
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74 </data>
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75 <!--
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76 <collection name="output_list" type="list" label="${tool.name} on ${on_string}: processed_data" structured_like="fastq_input" format="npz">
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77 <collection name="output_list" type="list" label="${tool.name} on ${on_string}: processed_data" format="npz">
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78 -->
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79 <collection name="output_list" type="list" label="${tool.name} on ${on_string}: processed_data">
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80 <!-- discover_datasets pattern="__name_and_ext__" directory="output" ext="npz" visible="false"/-->
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81 <discover_datasets pattern="(?P<designation>.+)\.npz" ext="hexrd.npz" directory="output"/>
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82 <!--discover_datasets pattern="(?P<designation>.+)\.npz" ext="npz" directory="output"/-->
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83 <!--discover_datasets pattern="(?P<designation>.npz)" ext="hexrd.npz" directory="output"/-->
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84 <!--filter>input_type_conditional['input_type'] == 'list_collection'</filter-->
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85 <filter>output_as_list == 'Yes'</filter>
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86 </collection>
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87 <data format="txt" name="output" label="${tool.name} on ${on_string}">
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88 <discover_datasets pattern="(?P<designation>.+)\.npz" directory="output" ext="hexrd.npz" visible="true" />
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89 <filter>output_as_list == 'No'</filter>
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90 </data>
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91 <!--data format="txt" name="output_list" label="${tool.name} on ${on_string}: listfiles">
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92 <filter>input_type_conditional['input_type'] == 'list_collection'</filter>
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93 </data -->
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94 </outputs>
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95 </tool>
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96
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