Mercurial > repos > bgruening > cp_cellprofiler

annotate cellprofiler.xml @ 0:ba4fd9fbf924 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author bgruening
date Thu, 26 Mar 2020 17:14:42 -0400
parents
children 78a16d8c8d5e
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0
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1 <tool id="cp_cellprofiler" name="cellProfiler" version="@CP_VERSION@">
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2 <description>runs a cellProfiler pipeline assembled by all the cellProfiler tools upstream in the workflow</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
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23 #for $i, $filename in enumerate($input_images):
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24 ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}'
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25 #end for
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26
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27 find `pwd`/input -name "*.*" > list.txt
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28 </configfile>
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29 </configfiles>
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30
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31 <inputs>
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32 <param name="pipeline" type="data" format="txt" label="Pipeline file" help="A ready-to-run .cppipe file. It can be created with various CellProfiler modules." />
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33 <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
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34 <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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35 </inputs>
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36
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37 <outputs>
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38 <collection name="pipeline_output" type="list" label="Cellprofiler pipeline output files">
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39 <discover_datasets pattern="__designation_and_ext__" visible="false" directory="output"/>
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40 </collection>
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41 <data format="txt" name="logs" from_work_dir="cp.log" label="CellProfiler log">
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42 <filter>detailed_output</filter>
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43 </data>
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44 </outputs>
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45
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46 <tests>
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47 <test expect_num_outputs="1">
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48 <param name="pipeline" value="ExampleHuman.cppipe" />
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49 <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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50 <param name="detailed_output" value="False" />
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51 <output_collection name="pipeline_output" type="list" count="7">
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52 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
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53 <assert_contents>
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54 <has_size value="183808"/>
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55 </assert_contents>
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56 </element>
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57 <element name="Cells">
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58 <expand macro="test_assert_content" n="290" />
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59 </element>
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60 <element name="Cytoplasm">
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61 <expand macro="test_assert_content" n="290" />
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62 </element>
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63 <element name="Experiment">
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64 <expand macro="test_assert_content" n="259" />
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65 </element>
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66 <element name="Image">
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67 <expand macro="test_assert_content" n="2" />
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68 </element>
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69 <element name="Nuclei">
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70 <expand macro="test_assert_content" n="290" />
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71 </element>
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72 <element name="PH3">
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73 <expand macro="test_assert_content" n="21" />
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74 </element>
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75 </output_collection>
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76 </test>
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77 <test expect_num_outputs="2">
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78 <param name="pipeline" value="ExampleHuman.cppipe" />
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79 <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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80 <param name="detailed_output" value="True" />
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81 <output_collection name="pipeline_output" type="list" count="7">
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82 <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
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83 <assert_contents>
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84 <has_size value="183808"/>
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85 </assert_contents>
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86 </element>
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87 <element name="Cells">
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88 <expand macro="test_assert_content" n="290" />
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89 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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90 <element name="Cytoplasm">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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91 <expand macro="test_assert_content" n="290" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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92 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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93 <element name="Experiment">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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94 <expand macro="test_assert_content" n="259" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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95 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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96 <element name="Image">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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97 <expand macro="test_assert_content" n="2" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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98 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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99 <element name="Nuclei">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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100 <expand macro="test_assert_content" n="290" />
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101 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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102 <element name="PH3">
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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103 <expand macro="test_assert_content" n="21" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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104 </element>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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105 </output_collection>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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106 <output name="logs" ftype='txt'>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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107 <assert_contents>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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108 <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"
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109 </assert_contents>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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110 </output>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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111 </test>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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112 </tests>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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113
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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114 <help>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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115 This tool runs a cellProfiler @CP_VERSION@ pipeline file.
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116
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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117 *** Parameters ***
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118
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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119 images: multi-select image files
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120
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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121 pipeline: cellProfiler pipeline file(.cppipe) file.
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122
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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123 *** Note ***
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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124
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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125 Only version @CP_VERSION@ pipeline can be run, other versions may cause problems.
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126
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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127 </help>
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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128 <expand macro="citations" />
ba4fd9fbf924 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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129 </tool>