Mercurial > repos > bgruening > cp_cellprofiler

comparison cellprofiler.xml @ 3:a98608f3abc5 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author bgruening
date Mon, 11 May 2020 07:50:04 -0400
parents 78a16d8c8d5e
children fca368c99299
comparison
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2:78a16d8c8d5e 3:a98608f3abc5
18 ]]></command> 18 ]]></command>
19 <configfiles> 19 <configfiles>
20 <configfile name="script_file"> 20 <configfile name="script_file">
21 mkdir ./input 21 mkdir ./input
22 mkdir ./output 22 mkdir ./output
23 #for $i, $filename in enumerate($input_images): 23
24 ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}' 24 #if $con_input_type.input_type =="yes"
25 #end for 25 tar -C ./input -xvf $con_input_type.input_images
26 #else
27 #for $i, $filename in enumerate($con_input_type.input_images):
28 ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}'
29 #end for
30 #end if
26 31
27 find `pwd`/input -name "*.*" > list.txt 32 find `pwd`/input -name "*.*" > list.txt
28 </configfile> 33 </configfile>
29 </configfiles> 34 </configfiles>
30 35
31 <inputs> 36 <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." /> 37 <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" /> 38 <conditional name="con_input_type">
39 <param name="input_type" type="select" label="Are the input images packed into a tar archive?">
40 <option value="yes">Yes</option>
41 <option value="no">No</option>
42 </param>
43 <when value="no">
44 <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
45 </when>
46 <when value="yes">
47 <param name="input_images" type="data" format="tar" label="A tarball of images" />
48 </when>
49 </conditional>
50
34 <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a detailed CellProfiler log file will be generated." /> 51 <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a detailed CellProfiler log file will be generated." />
35 </inputs> 52 </inputs>
36 53
37 <outputs> 54 <outputs>
38 <collection name="pipeline_output" type="list" label="CellProfiler pipeline output files"> 55 <collection name="pipeline_output" type="list" label="CellProfiler pipeline output files">
44 </outputs> 61 </outputs>
45 62
46 <tests> 63 <tests>
47 <test expect_num_outputs="1"> 64 <test expect_num_outputs="1">
48 <param name="pipeline" value="ExampleHuman.cppipe" /> 65 <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" /> 66 <conditional name="con_input_type">
67 <param name="input_type" value="no" />
68 <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
69 </conditional>
50 <param name="detailed_output" value="False" /> 70 <param name="detailed_output" value="False" />
51 <output_collection name="pipeline_output" type="list" count="7"> 71 <output_collection name="pipeline_output" type="list" count="7">
52 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay"> 72 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
53 <assert_contents> 73 <assert_contents>
54 <has_size value="183808"/> 74 <has_size value="183808"/>
74 </element> 94 </element>
75 </output_collection> 95 </output_collection>
76 </test> 96 </test>
77 <test expect_num_outputs="2"> 97 <test expect_num_outputs="2">
78 <param name="pipeline" value="ExampleHuman.cppipe" /> 98 <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" /> 99 <conditional name="con_input_type">
100 <param name="input_type" value="no" />
101 <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
102 </conditional>
80 <param name="detailed_output" value="True" /> 103 <param name="detailed_output" value="True" />
81 <output_collection name="pipeline_output" type="list" count="7"> 104 <output_collection name="pipeline_output" type="list" count="7">
82 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay"> 105 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
83 <assert_contents> 106 <assert_contents>
84 <has_size value="183808"/> 107 <has_size value="183808"/>
107 <assert_contents> 130 <assert_contents>
108 <has_text_matching expression="JVM will be started with AWT in headless mode" /> 131 <has_text_matching expression="JVM will be started with AWT in headless mode" />
109 </assert_contents> 132 </assert_contents>
110 </output> 133 </output>
111 </test> 134 </test>
135 <!-- Repeat tests for tarball input -->
136 <test expect_num_outputs="1">
137 <param name="pipeline" value="ExampleHuman.cppipe" />
138 <conditional name="con_input_type">
139 <param name="input_type" value="yes" />
140 <param name="input_images" value="images.tar" />
141 </conditional>
142 <param name="detailed_output" value="False" />
143 <output_collection name="pipeline_output" type="list" count="7">
144 <element name="AS_09125_050116030001_D03f00d0_Overlay">
145 <assert_contents>
146 <has_size value="183808"/>
147 </assert_contents>
148 </element>
149 <element name="Cells">
150 <expand macro="test_assert_content" n="290" />
151 </element>
152 <element name="Cytoplasm">
153 <expand macro="test_assert_content" n="290" />
154 </element>
155 <element name="Experiment">
156 <expand macro="test_assert_content" n="259" />
157 </element>
158 <element name="Image">
159 <expand macro="test_assert_content" n="2" />
160 </element>
161 <element name="Nuclei">
162 <expand macro="test_assert_content" n="290" />
163 </element>
164 <element name="PH3">
165 <expand macro="test_assert_content" n="21" />
166 </element>
167 </output_collection>
168 </test>
169 <test expect_num_outputs="2">
170 <param name="pipeline" value="ExampleHuman.cppipe" />
171 <conditional name="con_input_type">
172 <param name="input_type" value="yes" />
173 <param name="input_images" value="images.tar" />
174 </conditional>
175 <param name="detailed_output" value="True" />
176 <output_collection name="pipeline_output" type="list" count="7">
177 <element name="AS_09125_050116030001_D03f00d0_Overlay">
178 <assert_contents>
179 <has_size value="183808"/>
180 </assert_contents>
181 </element>
182 <element name="Cells">
183 <expand macro="test_assert_content" n="290" />
184 </element>
185 <element name="Cytoplasm">
186 <expand macro="test_assert_content" n="290" />
187 </element>
188 <element name="Experiment">
189 <expand macro="test_assert_content" n="259" />
190 </element>
191 <element name="Image">
192 <expand macro="test_assert_content" n="2" />
193 </element>
194 <element name="Nuclei">
195 <expand macro="test_assert_content" n="290" />
196 </element>
197 <element name="PH3">
198 <expand macro="test_assert_content" n="21" />
199 </element>
200 </output_collection>
201 <output name="logs" ftype='txt'>
202 <assert_contents>
203 <has_text_matching expression="JVM will be started with AWT in headless mode" />
204 </assert_contents>
205 </output>
206 </test>
207
112 </tests> 208 </tests>
113 209
114 <help> 210 <help>
115 This tool runs a CellProfiler @CP_VERSION@ pipeline file. 211 This tool runs a CellProfiler @CP_VERSION@ pipeline file.
116 212