Mercurial > repos > bgruening > cp_cellprofiler

annotate cellprofiler.xml @ 7:eb6c08714244 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:28:09 +0000
parents 0e4dccaafef5
children
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7
eb6c08714244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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1 <tool id="cp_cellprofiler" name="Run CellProfiler pipeline" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>with CellProfiler 3</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@">1</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 <edam_operations>
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13 <edam_operation>operation_3443</edam_operation>
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14 </edam_operations>
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15 <xrefs>
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16 <xref type="bio.tools">CellProfiler</xref>
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17 <xref type="biii">cellprofiler</xref>
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18 </xrefs>
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19 <expand macro="cp_requirements" />
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20 <command detect_errors="aggressive"><![CDATA[
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21 bash '$script_file' &&
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22 cellprofiler -c -r --file-list list.txt -o ./output -p '$pipeline'
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23 #if '$detailed_output'
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24 -L 10 > ./cp.log 2>&1
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25 #end if
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26 ]]></command>
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27 <configfiles>
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28 <configfile name="script_file">
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29 mkdir ./input
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30 mkdir ./output
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31
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32 #if $con_input_type.input_type =="yes"
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33 tar -C ./input -xvf $con_input_type.input_images
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34 #else
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35 #for $i, $filename in enumerate($con_input_type.input_images):
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36 ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}'
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37 #end for
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38 #end if
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39
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40 find `pwd`/input -name "*.*" > list.txt
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41 </configfile>
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42 </configfiles>
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43
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44 <inputs>
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45 <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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46 <conditional name="con_input_type">
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47 <param name="input_type" type="select" label="Are the input images packed into a tar archive?">
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48 <option value="yes">Yes</option>
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49 <option value="no">No</option>
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50 </param>
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51 <when value="no">
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52 <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
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53 </when>
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54 <when value="yes">
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55 <param name="input_images" type="data" format="tar" label="A tarball of images" />
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56 </when>
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57 </conditional>
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58
2
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59 <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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60 </inputs>
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61
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62 <outputs>
2
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63 <collection name="pipeline_output" type="list" label="CellProfiler pipeline output files">
0
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64 <discover_datasets pattern="__designation_and_ext__" visible="false" directory="output"/>
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65 </collection>
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66 <data format="txt" name="logs" from_work_dir="cp.log" label="CellProfiler log">
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67 <filter>detailed_output</filter>
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68 </data>
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69 </outputs>
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70
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71 <tests>
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72 <test expect_num_outputs="1">
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73 <param name="pipeline" value="ExampleHuman.cppipe" />
3
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74 <conditional name="con_input_type">
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75 <param name="input_type" value="no" />
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76 <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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77 </conditional>
0
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78 <param name="detailed_output" value="False" />
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79 <output_collection name="pipeline_output" type="list" count="7">
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80 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
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81 <assert_contents>
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82 <has_size value="183808"/>
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83 </assert_contents>
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84 </element>
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85 <element name="Cells">
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86 <expand macro="test_assert_content" n="290" />
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87 </element>
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88 <element name="Cytoplasm">
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89 <expand macro="test_assert_content" n="290" />
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90 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
91 <element name="Experiment">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
92 <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
93 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
94 <element name="Image">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
95 <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
96 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
97 <element name="Nuclei">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
98 <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
99 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
100 <element name="PH3">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
101 <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
102 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
103 </output_collection>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
104 </test>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
105 <test expect_num_outputs="2">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
106 <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
107 <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
108 <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
109 <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
110 </conditional>
0
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
111 <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
112 <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
113 <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
114 <assert_contents>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
115 <has_size value="183808"/>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
116 </assert_contents>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
117 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
118 <element name="Cells">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
119 <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
120 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
121 <element name="Cytoplasm">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
122 <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
123 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
124 <element name="Experiment">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
125 <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
126 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
127 <element name="Image">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
128 <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
129 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
130 <element name="Nuclei">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
131 <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
132 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
133 <element name="PH3">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
134 <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
135 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
136 </output_collection>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
137 <output name="logs" ftype='txt'>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
138 <assert_contents>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
139 <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
140 </assert_contents>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
141 </output>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
142 </test>
3
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
143 <!-- 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
144 <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
145 <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
146 <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
147 <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
148 <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
149 </conditional>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
150 <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
151 <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
152 <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
153 <assert_contents>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
154 <has_size value="183808"/>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
155 </assert_contents>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
156 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
157 <element name="Cells">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
158 <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
159 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
160 <element name="Cytoplasm">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
161 <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
162 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
163 <element name="Experiment">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
164 <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
165 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
166 <element name="Image">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
167 <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
168 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
169 <element name="Nuclei">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
170 <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
171 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
172 <element name="PH3">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
173 <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
174 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
175 </output_collection>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
176 </test>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
177 <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
178 <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
179 <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
180 <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
181 <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
182 </conditional>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
183 <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
184 <output_collection name="pipeline_output" type="list" count="7">
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185 <element name="AS_09125_050116030001_D03f00d0_Overlay">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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186 <assert_contents>
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187 <has_size value="183808"/>
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188 </assert_contents>
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189 </element>
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190 <element name="Cells">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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191 <expand macro="test_assert_content" n="290" />
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192 </element>
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193 <element name="Cytoplasm">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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194 <expand macro="test_assert_content" n="290" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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195 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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196 <element name="Experiment">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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197 <expand macro="test_assert_content" n="259" />
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198 </element>
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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199 <element name="Image">
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200 <expand macro="test_assert_content" n="2" />
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201 </element>
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202 <element name="Nuclei">
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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203 <expand macro="test_assert_content" n="290" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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204 </element>
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205 <element name="PH3">
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206 <expand macro="test_assert_content" n="21" />
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207 </element>
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208 </output_collection>
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209 <output name="logs" ftype='txt'>
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210 <assert_contents>
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211 <has_text_matching expression="JVM will be started with AWT in headless mode" />
a98608f3abc5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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212 </assert_contents>
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213 </output>
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214 </test>
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215
0
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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216 </tests>
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217
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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218 <help>
4
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219 <![CDATA[
fca368c99299 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
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220
fca368c99299 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
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221 .. class:: infomark
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222
fca368c99299 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
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223 **What it does**
0
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224
4
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225 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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226
fca368c99299 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
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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
fca368c99299 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
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230 **Input**
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231
fca368c99299 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
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232 - Collection of images.
0
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233
4
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234 - Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
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235
fca368c99299 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
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236 .. class:: infomark
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237
fca368c99299 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
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238 **Output**
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239
4
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240 - Images if the tool *SaveImages* was included in the workflow.
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241 - The features selected if the tool *ExportToSpreadsheet* was included in the workflow.
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242
fca368c99299 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
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243 .. class:: warningmark
0
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244
4
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245 **IMPORTANT**
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246
4
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247 Only the pipelines generated with the version @CP_VERSION@ of CellProfiler can be run, other versions may cause problems.
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248 ]]>
0
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249 </help>
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250 <expand macro="citations" />
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251 </tool>