Mercurial > repos > bgruening > cp_cellprofiler

comparison cellprofiler.xml @ 0:ba4fd9fbf924 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author bgruening
date Thu, 26 Mar 2020 17:14:42 -0400
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children 78a16d8c8d5e
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-1:000000000000 0:ba4fd9fbf924
1 <tool id="cp_cellprofiler" name="cellProfiler" version="@CP_VERSION@">
2 <description>runs a cellProfiler pipeline assembled by all the cellProfiler tools upstream in the workflow</description>
3 <macros>
4 <import>macros.xml</import>
5 <xml name="test_assert_content" token_n="291">
6 <assert_contents>
7 <has_n_lines n="@N@" />
8 </assert_contents>
9 </xml>
10 </macros>
11 <expand macro="cp_requirements" />
12 <command detect_errors="aggressive"><![CDATA[
13 bash '$script_file' &&
14 cellprofiler -c -r --file-list list.txt -o ./output -p '$pipeline'
15 #if '$detailed_output'
16 -L 10 > ./cp.log 2>&1
17 #end if
18 ]]></command>
19 <configfiles>
20 <configfile name="script_file">
21 mkdir ./input
22 mkdir ./output
23 #for $i, $filename in enumerate($input_images):
24 ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}'
25 #end for
26
27 find `pwd`/input -name "*.*" > list.txt
28 </configfile>
29 </configfiles>
30
31 <inputs>
32 <param name="pipeline" type="data" format="txt" label="Pipeline file" help="A ready-to-run .cppipe file. It can be created with various CellProfiler modules." />
33 <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
34 <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a detailed cellprofiler log file will be generated." />
35 </inputs>
36
37 <outputs>
38 <collection name="pipeline_output" type="list" label="Cellprofiler pipeline output files">
39 <discover_datasets pattern="__designation_and_ext__" visible="false" directory="output"/>
40 </collection>
41 <data format="txt" name="logs" from_work_dir="cp.log" label="CellProfiler log">
42 <filter>detailed_output</filter>
43 </data>
44 </outputs>
45
46 <tests>
47 <test expect_num_outputs="1">
48 <param name="pipeline" value="ExampleHuman.cppipe" />
49 <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
50 <param name="detailed_output" value="False" />
51 <output_collection name="pipeline_output" type="list" count="7">
52 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
53 <assert_contents>
54 <has_size value="183808"/>
55 </assert_contents>
56 </element>
57 <element name="Cells">
58 <expand macro="test_assert_content" n="290" />
59 </element>
60 <element name="Cytoplasm">
61 <expand macro="test_assert_content" n="290" />
62 </element>
63 <element name="Experiment">
64 <expand macro="test_assert_content" n="259" />
65 </element>
66 <element name="Image">
67 <expand macro="test_assert_content" n="2" />
68 </element>
69 <element name="Nuclei">
70 <expand macro="test_assert_content" n="290" />
71 </element>
72 <element name="PH3">
73 <expand macro="test_assert_content" n="21" />
74 </element>
75 </output_collection>
76 </test>
77 <test expect_num_outputs="2">
78 <param name="pipeline" value="ExampleHuman.cppipe" />
79 <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
80 <param name="detailed_output" value="True" />
81 <output_collection name="pipeline_output" type="list" count="7">
82 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
83 <assert_contents>
84 <has_size value="183808"/>
85 </assert_contents>
86 </element>
87 <element name="Cells">
88 <expand macro="test_assert_content" n="290" />
89 </element>
90 <element name="Cytoplasm">
91 <expand macro="test_assert_content" n="290" />
92 </element>
93 <element name="Experiment">
94 <expand macro="test_assert_content" n="259" />
95 </element>
96 <element name="Image">
97 <expand macro="test_assert_content" n="2" />
98 </element>
99 <element name="Nuclei">
100 <expand macro="test_assert_content" n="290" />
101 </element>
102 <element name="PH3">
103 <expand macro="test_assert_content" n="21" />
104 </element>
105 </output_collection>
106 <output name="logs" ftype='txt'>
107 <assert_contents>
108 <has_text_matching expression="JVM will be started with AWT in headless mode" />
109 </assert_contents>
110 </output>
111 </test>
112 </tests>
113
114 <help>
115 This tool runs a cellProfiler @CP_VERSION@ pipeline file.
116
117 *** Parameters ***
118
119 images: multi-select image files
120
121 pipeline: cellProfiler pipeline file(.cppipe) file.
122
123 *** Note ***
124
125 Only version @CP_VERSION@ pipeline can be run, other versions may cause problems.
126
127 </help>
128 <expand macro="citations" />
129 </tool>