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planemo upload for repository https://github.com/labsyspharm/basic-illumination commit 72a33d7c3ad18e717ec61c6b845099d69b9b7abd
author | goeckslab |
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date | Tue, 20 Sep 2022 17:34:14 +0000 |
parents | db20f09300bd |
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<tool id="basic_illumination" name="BaSiC Illumination" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>ImageJ BaSiC shading correction for use with Ashlar</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="version_cmd"/> <command detect_errors="aggressive"><![CDATA[ ln -s '$in_files' '${in_files.name}' && #set $outname = str('$in_files.name').replace('.ome.tiff','') @CMD_BEGIN@ "filename='${in_files.name}',output_dir='.',experiment_name='output'"; ]]></command> <inputs> <param type="data" name="in_files" format="tiff" label="Raw Cycle Images"/> </inputs> <outputs> <data format="tiff" name="output_dfp" label="${tool.name} on ${on_string}: DFP" from_work_dir="output-dfp.tif"/> <data format="tiff" name="output_ffp" label="${tool.name} on ${on_string}: FFP" from_work_dir="output-ffp.tif"/> </outputs> <tests> <test> <param name="in_files" value="test.tiff" /> <output name="output_dfp" ftype="tiff"> <assert_contents> <has_size value="350000" delta="50000" /> </assert_contents> </output> <output name="output_ffp" ftype="tiff"> <assert_contents> <has_size value="350000" delta="50000" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ ------------------- basic-illumination ------------------- **ImageJ BaSiC shading correction for use with Ashlar** **basic-illumination** can read image data directly from BioFormats-supported microscope vendor file formats as well as a directory of plain TIFF files. Output includes a flat field and dark field image per input file. ]]></help> <expand macro="citations" /> </tool>