Mercurial > repos > bgruening > cp_cellprofiler4

annotate cellprofiler.xml @ 3:77bc1c2e1b91 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit d18fae96f65d1b748fbd21b92b75ca3181fdd8bc
author bgruening
date Mon, 05 Aug 2024 15:30:07 +0000
parents f0656d0f2a4d
children
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5a810dc963f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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1 <tool id="cp_cellprofiler4" name="Run CellProfiler pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>with CellProfiler 4</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <xml name="test_assert_content" token_n="291">
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7 <assert_contents>
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8 <has_n_lines n="@N@" />
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9 </assert_contents>
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10 </xml>
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11 </macros>
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12 <expand macro="cp_requirements" />
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13 <command detect_errors="aggressive"><![CDATA[
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14 export MPLCONFIGDIR=\$TEMP &&
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15 bash '$script_file' &&
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16 cellprofiler -c -r --file-list list.txt -o ./output -p '$pipeline'
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17 #if $detailed_output
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18 -L 10 > ./cp.log 2>&1
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19 #end if
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20 ]]></command>
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21 <configfiles>
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22 <configfile name="script_file">
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23 mkdir ./input
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24 mkdir ./output
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26 #if $con_input_type.input_type =="yes"
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27 tar -C ./input -xvf $con_input_type.input_images
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28 #else
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29 #for $i, $filename in enumerate($con_input_type.input_images):
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30 ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}'
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31 #end for
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32 #end if
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33
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34 find `pwd`/input -name "*.*" > list.txt
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35 </configfile>
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36 </configfiles>
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37
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38 <inputs>
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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." />
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40 <conditional name="con_input_type">
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41 <param name="input_type" type="select" label="Are the input images packed into a tar archive?">
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42 <option value="yes">Yes</option>
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43 <option value="no">No</option>
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44 </param>
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45 <when value="no">
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46 <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
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47 </when>
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48 <when value="yes">
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49 <param name="input_images" type="data" format="tar" label="A tarball of images" />
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50 </when>
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51 </conditional>
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52
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53 <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a detailed CellProfiler log file will be generated." />
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54 </inputs>
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55
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56 <outputs>
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57 <collection name="pipeline_output" type="list" label="CellProfiler pipeline output files">
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58 <discover_datasets pattern="__designation_and_ext__" visible="false" directory="output"/>
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59 </collection>
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60 <data format="txt" name="logs" from_work_dir="cp.log" label="CellProfiler log">
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61 <filter>detailed_output</filter>
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62 </data>
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63 </outputs>
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64
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65 <tests>
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66 <test expect_num_outputs="1">
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67 <param name="pipeline" value="ExampleHuman.cppipe" />
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68 <conditional name="con_input_type">
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69 <param name="input_type" value="no" />
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70 <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
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71 </conditional>
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72 <param name="detailed_output" value="False" />
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73 <output_collection name="pipeline_output" type="list" count="7">
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74 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
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75 <assert_contents>
1
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76 <has_size value="182983"/>
0
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77 </assert_contents>
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78 </element>
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79 <element name="Cells">
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80 <expand macro="test_assert_content" n="290" />
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81 </element>
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82 <element name="Cytoplasm">
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83 <expand macro="test_assert_content" n="290" />
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84 </element>
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85 <element name="Experiment">
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86 <expand macro="test_assert_content" n="261" />
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87 </element>
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88 <element name="Image">
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89 <expand macro="test_assert_content" n="2" />
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90 </element>
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91 <element name="Nuclei">
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92 <expand macro="test_assert_content" n="290" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
93 </element>
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diff changeset
94 <element name="PH3">
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diff changeset
95 <expand macro="test_assert_content" n="23" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
96 </element>
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diff changeset
97 </output_collection>
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diff changeset
98 </test>
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bgruening
parents:
diff changeset
99 <test expect_num_outputs="2">
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bgruening
parents:
diff changeset
100 <param name="pipeline" value="ExampleHuman.cppipe" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
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diff changeset
101 <conditional name="con_input_type">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
102 <param name="input_type" value="no" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
103 <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
104 </conditional>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
105 <param name="detailed_output" value="True" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
106 <output_collection name="pipeline_output" type="list" count="7">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
107 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
108 <assert_contents>
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5a810dc963f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 0
diff changeset
109 <has_size value="182983"/>
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
110 </assert_contents>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
111 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
112 <element name="Cells">
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parents:
diff changeset
113 <expand macro="test_assert_content" n="290" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
114 </element>
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bgruening
parents:
diff changeset
115 <element name="Cytoplasm">
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bgruening
parents:
diff changeset
116 <expand macro="test_assert_content" n="290" />
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bgruening
parents:
diff changeset
117 </element>
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parents:
diff changeset
118 <element name="Experiment">
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diff changeset
119 <expand macro="test_assert_content" n="261" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
120 </element>
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bgruening
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diff changeset
121 <element name="Image">
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bgruening
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diff changeset
122 <expand macro="test_assert_content" n="2" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
123 </element>
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bgruening
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diff changeset
124 <element name="Nuclei">
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diff changeset
125 <expand macro="test_assert_content" n="290" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
126 </element>
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bgruening
parents:
diff changeset
127 <element name="PH3">
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parents:
diff changeset
128 <expand macro="test_assert_content" n="23" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
129 </element>
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bgruening
parents:
diff changeset
130 </output_collection>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
131 <output name="logs" ftype='txt'>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
132 <assert_contents>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
133 <has_text_matching expression="JVM will be started with AWT in headless mode" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
134 </assert_contents>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
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diff changeset
135 </output>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
136 </test>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
137 <!-- Repeat tests for tarball input -->
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
138 <test expect_num_outputs="1">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
139 <param name="pipeline" value="ExampleHuman.cppipe" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
140 <conditional name="con_input_type">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
141 <param name="input_type" value="yes" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
142 <param name="input_images" value="images.tar" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
143 </conditional>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
144 <param name="detailed_output" value="False" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
145 <output_collection name="pipeline_output" type="list" count="7">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
146 <element name="AS_09125_050116030001_D03f00d0_Overlay">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
147 <assert_contents>
1
5a810dc963f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 0
diff changeset
148 <has_size value="182983"/>
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
149 </assert_contents>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
150 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
151 <element name="Cells">
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parents:
diff changeset
152 <expand macro="test_assert_content" n="290" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
153 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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parents:
diff changeset
154 <element name="Cytoplasm">
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parents:
diff changeset
155 <expand macro="test_assert_content" n="290" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
156 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
157 <element name="Experiment">
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parents:
diff changeset
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
159 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
160 <element name="Image">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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parents:
diff changeset
161 <expand macro="test_assert_content" n="2" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
162 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
163 <element name="Nuclei">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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parents:
diff changeset
164 <expand macro="test_assert_content" n="290" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
165 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
166 <element name="PH3">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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parents:
diff changeset
167 <expand macro="test_assert_content" n="23" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
168 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
169 </output_collection>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
170 </test>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
171 <test expect_num_outputs="2">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
172 <param name="pipeline" value="ExampleHuman.cppipe" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
173 <conditional name="con_input_type">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
174 <param name="input_type" value="yes" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
175 <param name="input_images" value="images.tar" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
176 </conditional>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
177 <param name="detailed_output" value="True" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
178 <output_collection name="pipeline_output" type="list" count="7">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
179 <element name="AS_09125_050116030001_D03f00d0_Overlay">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
180 <assert_contents>
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5a810dc963f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 0
diff changeset
181 <has_size value="182983"/>
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
182 </assert_contents>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
183 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
184 <element name="Cells">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
185 <expand macro="test_assert_content" n="290" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
186 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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187 <element name="Cytoplasm">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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188 <expand macro="test_assert_content" n="290" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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189 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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190 <element name="Experiment">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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191 <expand macro="test_assert_content" n="261" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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192 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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193 <element name="Image">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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194 <expand macro="test_assert_content" n="2" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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195 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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196 <element name="Nuclei">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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197 <expand macro="test_assert_content" n="290" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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198 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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199 <element name="PH3">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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200 <expand macro="test_assert_content" n="23" />
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201 </element>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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202 </output_collection>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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203 <output name="logs" ftype='txt'>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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204 <assert_contents>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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205 <has_text_matching expression="JVM will be started with AWT in headless mode" />
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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206 </assert_contents>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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207 </output>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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208 </test>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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209
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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210 </tests>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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211
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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212 <help>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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213 <![CDATA[
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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214
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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215 .. class:: infomark
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216
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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217 **What it does**
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218
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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219 This is the last tool in a CellProfiler workflow and runs a CellProfiler @TOOL_VERSION@ pipeline file on a collection of images.
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220
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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221
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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222 .. class:: infomark
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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223
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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224 **Input**
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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225
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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226 - Collection of images.
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227
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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228 - Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
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229
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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230 .. class:: infomark
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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231
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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232 **Output**
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233
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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234 - Images if the tool *SaveImages* was included in the workflow.
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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235 - The features selected if the tool *ExportToSpreadsheet* was included in the workflow.
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236
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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237 .. class:: warningmark
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238
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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239 **IMPORTANT**
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240
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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241 Only the pipelines generated with the version @TOOL_VERSION@ of CellProfiler can be run, other versions may cause problems.
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242 ]]>
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243 </help>
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244 <expand macro="citations" />
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245 </tool>