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comparison chess_preprocessor.xml @ 0:4d2a2268a17a draft

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"planemo upload"
author mzhuang
date Thu, 23 Sep 2021 21:00:48 +0000
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children 0545899061d3
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-1:000000000000 0:4d2a2268a17a
1 <tool id="chess_preprocessor" name="CHESS Pre-processing Tool" version="0.1.0">
2 <description>for pre-processing raw data</description>
3 <requirements>
4 <requirement type="package" version="0.8.4">hexrd</requirement>
5 </requirements>
6 <command><![CDATA[
7 #import os.path
8
9 ##source ~/.bashrc;conda activate pulsar;
10 ##source ~/.bashrc; conda activate __hexrd@0.8.0;
11 mkdir -p output;
12 cd output;
13 #set $history_id=$__app__.security.encode_id($output.creating_job.history.id)
14 echo '$history_id' >> '$output';
15
16 #if $input_source_conditional.input_source == "input_source_history"
17 #set $input_type = $input_source_conditional.input_type_conditional.input_type
18 #if $input_type == "single"
19 #set $input_data = $input_source_conditional.input_type_conditional.fastq_input1
20 #elif $input_type == "list_collection"
21 #set $input_data = $input_source_conditional.input_type_conditional.fastq_input
22 #end if#
23
24 #set $var = ""
25 #for $f in $input_data#
26 #set $var += "${f}\n"
27 #end for#
28 #set files = '\\n'.join([str($file) for $file in $input_data])
29 ##for $f in $input_data#
30 #if $output_as_list == "Yes"
31 ##printf "$files" >> '$output_list_log' 2>&1;
32 printf "$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;
33 #elif $output_as_list == "No"
34 printf "$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;
35 #end if#
36 ##end for#
37 #elif $input_source_conditional.input_source == "input_source_linux"
38 #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])]
39 ##set $scanlist = '\n'.join($scans)
40
41 #for $n in $scans#
42 #if $output_as_list == "Yes"
43 echo '$input_source_conditional.base_dir' >> '$output_list_log';
44 python '$__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;
45 #elif $output_as_list == "No"
46 echo '$input_source_conditional.base_dir' >> '$output';
47 python '__tool_directory__/preprocess_dexela_h5_filesystem.py' '$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;
48 #end if#
49 #end for#
50 #end if#
51 conda deactivate
52 ]]></command>
53 <inputs>
54 <!--
55 <param name="infile_" type="data" multiple="true" label="Any file"/>
56 -->
57 <conditional name="input_source_conditional">
58 <param name="input_source" type="select" label="Location of raw data">
59 <option value="input_source_history" selected="true">Choose from History panel</option>
60 <option value="input_source_linux">Specify a directory in CHESS file system </option>
61 </param>
62 <when value="input_source_history">
63 <conditional name="input_type_conditional">
64 <param name="input_type" type="select" label="Input raw data as">
65 <option value="list_collection" selected="true">List of Datasets</option>
66 <option value="single">Dataset(s)</option>
67 </param>
68 <when value="single">
69 <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"/>
70 </when>
71 <when value="list_collection">
72 <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"/>
73 </when>
74 </conditional>
75 </when>
76 <when value="input_source_linux">
77 <param name="base_dir" type="text" label="Please specify the directory that contains raw data">
78 <sanitizer>
79 <valid initial="string.ascii_letters,string.digits">
80 <add value="#,/,*,@,.,_,-" />
81 <add value="_" />
82 </valid>
83 </sanitizer>
84 </param>
85 <param name="expt_name" type="text" label="Please specify the experiment name"/>
86 <param name="samp_name" type="text" label="Please specify the sample name"/>
87 <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)"/>
88 </when>
89 </conditional>
90 <!--
91 <param name="which_cluster" type="select" label="Send your job to below cluster">
92 <option value="SDSC" selected="true">SDSC</option>
93 <option value="Cornell" selected="true">Cornell CHESS</option>
94 </param>
95 -->
96 <!--
97 <param name="output_dir" type="text" hidden="true"/>
98 -->
99 <param name="num_frames" type="integer" value="999" label="Number of frames to read"/>
100 <param name="start_frame" type="integer" value="0" label="Index of first data frame"/>
101 <param name="threshold" type="integer" value="50" label="Threshold for frame caches"/>
102 <param name="ome_start" type="float" value="-50.0" label="Start omega"/>
103 <param name="ome_end" type="float" value="49.9" label="End omega"/>
104 <param name="output_as_list" type="select" label="Would you like the tool to output result(s) as a list?">
105 <option value="Yes" selected="true">Yes. Let the results be contained in a list.</option>
106 <option value="No" >No. Show them individually.</option>
107 </param>
108 </inputs>
109 <outputs>
110 <data format="txt" name="output_list_log" label="${tool.name} on ${on_string}">
111 <!--filter>input_type_conditional['input_type'] == 'single'</filter-->
112 <filter>output_as_list == 'Yes'</filter>
113 </data>
114 <!--
115 <collection name="output_list" type="list" label="${tool.name} on ${on_string}: processed_data" structured_like="fastq_input" format="npz">
116 <collection name="output_list" type="list" label="${tool.name} on ${on_string}: processed_data" format="npz">
117 -->
118 <collection name="output_list" type="list" label="${tool.name} on ${on_string}: processed_data">
119 <!-- discover_datasets pattern="__name_and_ext__" directory="output" ext="npz" visible="false"/-->
120 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.npz" ext="hexrd.npz" directory="output"/>
121 <!--discover_datasets pattern="(?P&lt;designation&gt;.+)\.npz" ext="npz" directory="output"/-->
122 <!--discover_datasets pattern="(?P&lt;designation&gt;.npz)" ext="hexrd.npz" directory="output"/-->
123 <!--filter>input_type_conditional['input_type'] == 'list_collection'</filter-->
124 <filter>output_as_list == 'Yes'</filter>
125 </collection>
126 <data format="txt" name="output" label="${tool.name} on ${on_string}">
127 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.npz" directory="output" ext="hexrd.npz" visible="true" />
128 <filter>output_as_list == 'No'</filter>
129 </data>
130 <!--data format="txt" name="output_list" label="${tool.name} on ${on_string}: listfiles">
131 <filter>input_type_conditional['input_type'] == 'list_collection'</filter>
132 </data -->
133 </outputs>
134 </tool>
135