Mercurial > repos > bgruening > cp_cellprofiler

comparison cellprofiler.xml @ 2:78a16d8c8d5e draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
author bgruening
date Thu, 16 Apr 2020 05:40:08 -0400
parents ba4fd9fbf924
children a98608f3abc5
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1:0b8f8406ee16 2:78a16d8c8d5e
1 <tool id="cp_cellprofiler" name="cellProfiler" version="@CP_VERSION@"> 1 <tool id="cp_cellprofiler" name="CellProfiler" version="@CP_VERSION@">
2 <description>runs a cellProfiler pipeline assembled by all the cellProfiler tools upstream in the workflow</description> 2 <description>run a CellProfiler pipeline</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="test_assert_content" token_n="291"> 5 <xml name="test_assert_content" token_n="291">
6 <assert_contents> 6 <assert_contents>
7 <has_n_lines n="@N@" /> 7 <has_n_lines n="@N@" />
29 </configfiles> 29 </configfiles>
30 30
31 <inputs> 31 <inputs>
32 <param name="pipeline" type="data" format="txt" label="Pipeline file" help="A ready-to-run .cppipe file. It can be created with various CellProfiler modules." /> 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." />
33 <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" /> 33 <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
34 <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a detailed cellprofiler log file will be generated." /> 34 <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a detailed CellProfiler log file will be generated." />
35 </inputs> 35 </inputs>
36 36
37 <outputs> 37 <outputs>
38 <collection name="pipeline_output" type="list" label="Cellprofiler pipeline output files"> 38 <collection name="pipeline_output" type="list" label="CellProfiler pipeline output files">
39 <discover_datasets pattern="__designation_and_ext__" visible="false" directory="output"/> 39 <discover_datasets pattern="__designation_and_ext__" visible="false" directory="output"/>
40 </collection> 40 </collection>
41 <data format="txt" name="logs" from_work_dir="cp.log" label="CellProfiler log"> 41 <data format="txt" name="logs" from_work_dir="cp.log" label="CellProfiler log">
42 <filter>detailed_output</filter> 42 <filter>detailed_output</filter>
43 </data> 43 </data>
110 </output> 110 </output>
111 </test> 111 </test>
112 </tests> 112 </tests>
113 113
114 <help> 114 <help>
115 This tool runs a cellProfiler @CP_VERSION@ pipeline file. 115 This tool runs a CellProfiler @CP_VERSION@ pipeline file.
116 116
117 *** Parameters *** 117 *** Parameters ***
118 118
119 images: multi-select image files 119 images: multi-select image files
120 120
121 pipeline: cellProfiler pipeline file(.cppipe) file. 121 pipeline: CellProfiler pipeline file(.cppipe) file.
122 122
123 *** Note *** 123 *** Note ***
124 124
125 Only version @CP_VERSION@ pipeline can be run, other versions may cause problems. 125 Only version @CP_VERSION@ pipeline can be run, other versions may cause problems.
126 126