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comparison basic_illumination.xml @ 0:fd8dfd64f25e draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
author perssond
date Fri, 12 Mar 2021 00:13:46 +0000
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-1:000000000000 0:fd8dfd64f25e
1 <tool id="basic_illumination" name="BaSiC Illumination" version="@VERSION@.3" profile="17.09">
2 <description>ImageJ BaSiC shading correction for use with Ashlar</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements"/>
8 @VERSION_CMD@
9
10 <command detect_errors="exit_code"><![CDATA[
11 ln -s $in_files "${in_files.name}" &&
12
13 #set $outname = str($in_files.name).replace('.ome.tiff','')
14
15 @CMD_BEGIN@
16
17 "filename='${in_files.name}',output_dir='.',experiment_name='output'";
18
19 ]]></command>
20
21 <inputs>
22 <param type="data" name="in_files" format="tiff" label="Raw Cycle Images"/>
23 </inputs>
24
25 <outputs>
26 <data format="tiff" name="output_dfp" label="${tool.name} on ${on_string}: DFP" from_work_dir="output-dfp.tif"/>
27 <data format="tiff" name="output_ffp" label="${tool.name} on ${on_string}: FFP" from_work_dir="output-ffp.tif"/>
28 </outputs>
29
30 <help><![CDATA[
31 basic-illumination
32 ImageJ BaSiC shading correction for use with Ashlar
33
34 Running as a Docker container
35 Create a container:
36
37 docker run -it -v /path/to/data:/data labsyspharm/basic-illumination bash
38 (where /path/to/data is the data directory on your local machine. Your data will be mapped to /data inside the container)
39
40 Once inside the container, do ls /data to ensure your data is there, followed by
41
42 ImageJ-linux64 --ij2 --headless --run imagej_basic_ashlar.py \
43 "filename='/data/input.ome.tiff',output_dir='/data/',experiment_name='my_experiment'"
44 for each input.ome.tiff in your data directory.
45
46 OHSU Wrapper Repo: https://github.com/ohsu-comp-bio/basic-illumination
47 Conda Package Available From: https://anaconda.org/ohsu-comp-bio/basic-illumination
48 ]]></help>
49 <expand macro="citations" />
50 </tool>