Mercurial > repos > bgruening > cp_cellprofiler4

comparison cellprofiler.xml @ 0:b333df978624 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
author bgruening
date Mon, 25 Apr 2022 18:30:59 +0000
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children 5a810dc963f4
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-1:000000000000 0:b333df978624
1 <tool id="cp_cellprofiler4" name="CellProfiler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>run a CellProfiler pipeline</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@VERSION_SUFFIX@">0</token>
6 <xml name="test_assert_content" token_n="291">
7 <assert_contents>
8 <has_n_lines n="@N@" />
9 </assert_contents>
10 </xml>
11 </macros>
12 <expand macro="cp_requirements" />
13 <command detect_errors="aggressive"><![CDATA[
14 export MPLCONFIGDIR=\$TEMP &&
15 bash '$script_file' &&
16 cellprofiler -c -r --file-list list.txt -o ./output -p '$pipeline'
17 #if $detailed_output
18 -L 10 > ./cp.log 2>&1
19 #end if
20 ]]></command>
21 <configfiles>
22 <configfile name="script_file">
23 mkdir ./input
24 mkdir ./output
25
26 #if $con_input_type.input_type =="yes"
27 tar -C ./input -xvf $con_input_type.input_images
28 #else
29 #for $i, $filename in enumerate($con_input_type.input_images):
30 ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}'
31 #end for
32 #end if
33
34 find `pwd`/input -name "*.*" > list.txt
35 </configfile>
36 </configfiles>
37
38 <inputs>
39 <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." />
40 <conditional name="con_input_type">
41 <param name="input_type" type="select" label="Are the input images packed into a tar archive?">
42 <option value="yes">Yes</option>
43 <option value="no">No</option>
44 </param>
45 <when value="no">
46 <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
47 </when>
48 <when value="yes">
49 <param name="input_images" type="data" format="tar" label="A tarball of images" />
50 </when>
51 </conditional>
52
53 <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a detailed CellProfiler log file will be generated." />
54 </inputs>
55
56 <outputs>
57 <collection name="pipeline_output" type="list" label="CellProfiler pipeline output files">
58 <discover_datasets pattern="__designation_and_ext__" visible="false" directory="output"/>
59 </collection>
60 <data format="txt" name="logs" from_work_dir="cp.log" label="CellProfiler log">
61 <filter>detailed_output</filter>
62 </data>
63 </outputs>
64
65 <tests>
66 <test expect_num_outputs="1">
67 <param name="pipeline" value="ExampleHuman.cppipe" />
68 <conditional name="con_input_type">
69 <param name="input_type" value="no" />
70 <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
71 </conditional>
72 <param name="detailed_output" value="False" />
73 <output_collection name="pipeline_output" type="list" count="7">
74 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
75 <assert_contents>
76 <has_size value="168221"/>
77 </assert_contents>
78 </element>
79 <element name="Cells">
80 <expand macro="test_assert_content" n="290" />
81 </element>
82 <element name="Cytoplasm">
83 <expand macro="test_assert_content" n="290" />
84 </element>
85 <element name="Experiment">
86 <expand macro="test_assert_content" n="261" />
87 </element>
88 <element name="Image">
89 <expand macro="test_assert_content" n="2" />
90 </element>
91 <element name="Nuclei">
92 <expand macro="test_assert_content" n="290" />
93 </element>
94 <element name="PH3">
95 <expand macro="test_assert_content" n="23" />
96 </element>
97 </output_collection>
98 </test>
99 <test expect_num_outputs="2">
100 <param name="pipeline" value="ExampleHuman.cppipe" />
101 <conditional name="con_input_type">
102 <param name="input_type" value="no" />
103 <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
104 </conditional>
105 <param name="detailed_output" value="True" />
106 <output_collection name="pipeline_output" type="list" count="7">
107 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
108 <assert_contents>
109 <has_size value="168221"/>
110 </assert_contents>
111 </element>
112 <element name="Cells">
113 <expand macro="test_assert_content" n="290" />
114 </element>
115 <element name="Cytoplasm">
116 <expand macro="test_assert_content" n="290" />
117 </element>
118 <element name="Experiment">
119 <expand macro="test_assert_content" n="261" />
120 </element>
121 <element name="Image">
122 <expand macro="test_assert_content" n="2" />
123 </element>
124 <element name="Nuclei">
125 <expand macro="test_assert_content" n="290" />
126 </element>
127 <element name="PH3">
128 <expand macro="test_assert_content" n="23" />
129 </element>
130 </output_collection>
131 <output name="logs" ftype='txt'>
132 <assert_contents>
133 <has_text_matching expression="JVM will be started with AWT in headless mode" />
134 </assert_contents>
135 </output>
136 </test>
137 <!-- Repeat tests for tarball input -->
138 <test expect_num_outputs="1">
139 <param name="pipeline" value="ExampleHuman.cppipe" />
140 <conditional name="con_input_type">
141 <param name="input_type" value="yes" />
142 <param name="input_images" value="images.tar" />
143 </conditional>
144 <param name="detailed_output" value="False" />
145 <output_collection name="pipeline_output" type="list" count="7">
146 <element name="AS_09125_050116030001_D03f00d0_Overlay">
147 <assert_contents>
148 <has_size value="168221"/>
149 </assert_contents>
150 </element>
151 <element name="Cells">
152 <expand macro="test_assert_content" n="290" />
153 </element>
154 <element name="Cytoplasm">
155 <expand macro="test_assert_content" n="290" />
156 </element>
157 <element name="Experiment">
158 <expand macro="test_assert_content" n="261" />
159 </element>
160 <element name="Image">
161 <expand macro="test_assert_content" n="2" />
162 </element>
163 <element name="Nuclei">
164 <expand macro="test_assert_content" n="290" />
165 </element>
166 <element name="PH3">
167 <expand macro="test_assert_content" n="23" />
168 </element>
169 </output_collection>
170 </test>
171 <test expect_num_outputs="2">
172 <param name="pipeline" value="ExampleHuman.cppipe" />
173 <conditional name="con_input_type">
174 <param name="input_type" value="yes" />
175 <param name="input_images" value="images.tar" />
176 </conditional>
177 <param name="detailed_output" value="True" />
178 <output_collection name="pipeline_output" type="list" count="7">
179 <element name="AS_09125_050116030001_D03f00d0_Overlay">
180 <assert_contents>
181 <has_size value="168221"/>
182 </assert_contents>
183 </element>
184 <element name="Cells">
185 <expand macro="test_assert_content" n="290" />
186 </element>
187 <element name="Cytoplasm">
188 <expand macro="test_assert_content" n="290" />
189 </element>
190 <element name="Experiment">
191 <expand macro="test_assert_content" n="261" />
192 </element>
193 <element name="Image">
194 <expand macro="test_assert_content" n="2" />
195 </element>
196 <element name="Nuclei">
197 <expand macro="test_assert_content" n="290" />
198 </element>
199 <element name="PH3">
200 <expand macro="test_assert_content" n="23" />
201 </element>
202 </output_collection>
203 <output name="logs" ftype='txt'>
204 <assert_contents>
205 <has_text_matching expression="JVM will be started with AWT in headless mode" />
206 </assert_contents>
207 </output>
208 </test>
209
210 </tests>
211
212 <help>
213 <![CDATA[
214
215 .. class:: infomark
216
217 **What it does**
218
219 This is the last tool in a CellProfiler workflow and runs a CellProfiler @TOOL_VERSION@ pipeline file on a collection of images.
220
221
222 .. class:: infomark
223
224 **Input**
225
226 - Collection of images.
227
228 - Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
229
230 .. class:: infomark
231
232 **Output**
233
234 - Images if the tool *SaveImages* was included in the workflow.
235 - The features selected if the tool *ExportToSpreadsheet* was included in the workflow.
236
237 .. class:: warningmark
238
239 **IMPORTANT**
240
241 Only the pipelines generated with the version @TOOL_VERSION@ of CellProfiler can be run, other versions may cause problems.
242 ]]>
243 </help>
244 <expand macro="citations" />
245 </tool>