Mercurial > repos > bgruening > cp_tile
view macros.xml @ 1:878bafb411dd draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author | bgruening |
---|---|
date | Fri, 26 Feb 2021 14:13:03 +0000 |
parents | 33bf7aa4e684 |
children |
line wrap: on
line source
<macros> <token name="@CP_VERSION@">3.1.9</token> <token name="@PY_VERSION@">3.7</token> <token name="@FORMATS@">jpg,png,tiff,bmp,gif,pcx,ppm,psd,pbm,pgm,eps</token> <token name="@SPACES@">" "</token> <!-- four spaces needed for CP pipeline file --> <token name="@COMMON_HELP@"> .. class:: infomark **Input** Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools. .. class:: infomark **Output** The input CellProfiler pipeline file *(.cppipe)* in addition to the settings of this module. .. class:: warningmark **IMPORTANT** The first tool in a CellProfiler workflow has to be **Starting modules** and the last one **CellProfiler**. You can also execute the entire pipeline with the final CellProfiler tool, in which you feed in the images you want to process as well. </token> <xml name="output_pipeline_param"> <data name="output_pipeline" from_work_dir="output.cppipe" format="txt"/> </xml> <xml name="input_pipeline_param"> <param name="input_pipeline" type="data" format="data" label="Select the input CellProfiler pipeline"/> </xml> <xml name="cp_requirements"> <requirements> <requirement type="package" version="@CP_VERSION@">cellprofiler</requirement> </requirements> </xml> <xml name="py_requirements"> <requirements> <requirement type="package" version="@PY_VERSION@">python</requirement> </requirements> </xml> <xml name="citations"> <citations> <citation type="bibtex"> @article{McQuin_2018, title = {CellProfiler 3.0: Next-generation image processing for biology}, author = {McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE}, year = {2018}, volume = {16(7):e2005970}, DOI = {10.1371/journal.pbio.2005970}, journal = {PLoS Biol.}, url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970}, } </citation> </citations> </xml> <xml name="cmd_modules"> <command detect_errors="aggressive"> <![CDATA[ python '$script_file' '$inputs' '$input_pipeline' ]]> </command> </xml> <xml name="text_validator"> <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator> </xml> <xml name="test_input_pipeline_param"> <param name="input_pipeline" value="common.cppipe" /> </xml> <xml name="test_out_file" token_file="common.cppipe"> <output name="output_pipeline" ftype="txt" file="@FILE@" lines_diff="0"/> </xml> </macros>