Mercurial > repos > bgruening > cp_cellprofiler

annotate cellprofiler.xml @ 4:fca368c99299 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
author bgruening
date Fri, 29 May 2020 18:16:51 -0400
parents a98608f3abc5
children 0e4dccaafef5
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1 <tool id="cp_cellprofiler" name="CellProfiler" version="@CP_VERSION@">
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2 <description>run a CellProfiler pipeline</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="test_assert_content" token_n="291">
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6 <assert_contents>
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7 <has_n_lines n="@N@" />
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8 </assert_contents>
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9 </xml>
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10 </macros>
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11 <expand macro="cp_requirements" />
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12 <command detect_errors="aggressive"><![CDATA[
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13 bash '$script_file' &&
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14 cellprofiler -c -r --file-list list.txt -o ./output -p '$pipeline'
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15 #if '$detailed_output'
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16 -L 10 > ./cp.log 2>&1
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17 #end if
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18 ]]></command>
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19 <configfiles>
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20 <configfile name="script_file">
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21 mkdir ./input
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22 mkdir ./output
3
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23
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24 #if $con_input_type.input_type =="yes"
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25 tar -C ./input -xvf $con_input_type.input_images
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26 #else
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27 #for $i, $filename in enumerate($con_input_type.input_images):
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28 ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}'
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29 #end for
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30 #end if
0
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31
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32 find `pwd`/input -name "*.*" > list.txt
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33 </configfile>
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34 </configfiles>
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35
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36 <inputs>
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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." />
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38 <conditional name="con_input_type">
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39 <param name="input_type" type="select" label="Are the input images packed into a tar archive?">
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40 <option value="yes">Yes</option>
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41 <option value="no">No</option>
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42 </param>
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43 <when value="no">
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44 <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
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45 </when>
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46 <when value="yes">
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47 <param name="input_images" type="data" format="tar" label="A tarball of images" />
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48 </when>
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49 </conditional>
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50
2
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51 <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a detailed CellProfiler log file will be generated." />
0
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52 </inputs>
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53
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54 <outputs>
2
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55 <collection name="pipeline_output" type="list" label="CellProfiler pipeline output files">
0
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56 <discover_datasets pattern="__designation_and_ext__" visible="false" directory="output"/>
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57 </collection>
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58 <data format="txt" name="logs" from_work_dir="cp.log" label="CellProfiler log">
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59 <filter>detailed_output</filter>
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60 </data>
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61 </outputs>
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62
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63 <tests>
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64 <test expect_num_outputs="1">
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65 <param name="pipeline" value="ExampleHuman.cppipe" />
3
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66 <conditional name="con_input_type">
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67 <param name="input_type" value="no" />
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68 <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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69 </conditional>
0
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70 <param name="detailed_output" value="False" />
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71 <output_collection name="pipeline_output" type="list" count="7">
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72 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
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73 <assert_contents>
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74 <has_size value="183808"/>
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75 </assert_contents>
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76 </element>
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77 <element name="Cells">
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78 <expand macro="test_assert_content" n="290" />
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79 </element>
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80 <element name="Cytoplasm">
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81 <expand macro="test_assert_content" n="290" />
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82 </element>
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83 <element name="Experiment">
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84 <expand macro="test_assert_content" n="259" />
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85 </element>
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86 <element name="Image">
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87 <expand macro="test_assert_content" n="2" />
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88 </element>
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89 <element name="Nuclei">
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90 <expand macro="test_assert_content" n="290" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
91 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
92 <element name="PH3">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
93 <expand macro="test_assert_content" n="21" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
94 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
95 </output_collection>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
96 </test>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
97 <test expect_num_outputs="2">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
98 <param name="pipeline" value="ExampleHuman.cppipe" />
3
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
99 <conditional name="con_input_type">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
100 <param name="input_type" value="no" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
101 <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
102 </conditional>
0
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
103 <param name="detailed_output" value="True" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
104 <output_collection name="pipeline_output" type="list" count="7">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
105 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
106 <assert_contents>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
107 <has_size value="183808"/>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
108 </assert_contents>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
109 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
110 <element name="Cells">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
111 <expand macro="test_assert_content" n="290" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
112 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
113 <element name="Cytoplasm">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
114 <expand macro="test_assert_content" n="290" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
115 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
116 <element name="Experiment">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
117 <expand macro="test_assert_content" n="259" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
118 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
119 <element name="Image">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
120 <expand macro="test_assert_content" n="2" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
121 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
122 <element name="Nuclei">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
123 <expand macro="test_assert_content" n="290" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
124 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
125 <element name="PH3">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
126 <expand macro="test_assert_content" n="21" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
127 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
128 </output_collection>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
129 <output name="logs" ftype='txt'>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
130 <assert_contents>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
131 <has_text_matching expression="JVM will be started with AWT in headless mode" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
132 </assert_contents>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
133 </output>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
134 </test>
3
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
135 <!-- Repeat tests for tarball input -->
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
136 <test expect_num_outputs="1">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
137 <param name="pipeline" value="ExampleHuman.cppipe" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
138 <conditional name="con_input_type">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
139 <param name="input_type" value="yes" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
140 <param name="input_images" value="images.tar" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
141 </conditional>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
142 <param name="detailed_output" value="False" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
143 <output_collection name="pipeline_output" type="list" count="7">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
144 <element name="AS_09125_050116030001_D03f00d0_Overlay">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
145 <assert_contents>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
146 <has_size value="183808"/>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
147 </assert_contents>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
148 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
149 <element name="Cells">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
150 <expand macro="test_assert_content" n="290" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
151 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
152 <element name="Cytoplasm">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
153 <expand macro="test_assert_content" n="290" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
154 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
155 <element name="Experiment">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
156 <expand macro="test_assert_content" n="259" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
157 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
158 <element name="Image">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
159 <expand macro="test_assert_content" n="2" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
160 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
161 <element name="Nuclei">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
162 <expand macro="test_assert_content" n="290" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
163 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
164 <element name="PH3">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
165 <expand macro="test_assert_content" n="21" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
166 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
167 </output_collection>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
168 </test>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
169 <test expect_num_outputs="2">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
170 <param name="pipeline" value="ExampleHuman.cppipe" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
171 <conditional name="con_input_type">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
172 <param name="input_type" value="yes" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
173 <param name="input_images" value="images.tar" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
174 </conditional>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
175 <param name="detailed_output" value="True" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
176 <output_collection name="pipeline_output" type="list" count="7">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
177 <element name="AS_09125_050116030001_D03f00d0_Overlay">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
178 <assert_contents>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
179 <has_size value="183808"/>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
180 </assert_contents>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
181 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
182 <element name="Cells">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
183 <expand macro="test_assert_content" n="290" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
184 </element>
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185 <element name="Cytoplasm">
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186 <expand macro="test_assert_content" n="290" />
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187 </element>
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188 <element name="Experiment">
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189 <expand macro="test_assert_content" n="259" />
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190 </element>
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191 <element name="Image">
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192 <expand macro="test_assert_content" n="2" />
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193 </element>
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194 <element name="Nuclei">
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195 <expand macro="test_assert_content" n="290" />
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196 </element>
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197 <element name="PH3">
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198 <expand macro="test_assert_content" n="21" />
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199 </element>
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200 </output_collection>
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201 <output name="logs" ftype='txt'>
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202 <assert_contents>
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203 <has_text_matching expression="JVM will be started with AWT in headless mode" />
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204 </assert_contents>
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205 </output>
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206 </test>
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207
0
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208 </tests>
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209
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210 <help>
4
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211 <![CDATA[
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212
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213 .. class:: infomark
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214
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215 **What it does**
0
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216
4
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217 This is the last tool in a CellProfiler workflow and runs a CellProfiler @CP_VERSION@ pipeline file on a collection of images.
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218
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219
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220 .. class:: infomark
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221
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222 **Input**
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223
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224 - Collection of images.
0
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225
4
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226 - Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
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227
fca368c99299 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
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228 .. class:: infomark
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229
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230 **Output**
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231
4
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232 - Images if the tool *SaveImages* was included in the workflow.
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233 - The features selected if the tool *ExportToSpreadsheet* was included in the workflow.
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234
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235 .. class:: warningmark
0
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236
4
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237 **IMPORTANT**
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238
4
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239 Only the pipelines generated with the version @CP_VERSION@ of CellProfiler can be run, other versions may cause problems.
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240 ]]>
0
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241 </help>
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242 <expand macro="citations" />
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243 </tool>