Mercurial > repos > bgruening > cp_cellprofiler
comparison cellprofiler.xml @ 3:a98608f3abc5 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author | bgruening |
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date | Mon, 11 May 2020 07:50:04 -0400 |
parents | 78a16d8c8d5e |
children | fca368c99299 |
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2:78a16d8c8d5e | 3:a98608f3abc5 |
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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 |