Mercurial > repos > tduigou > icfree_extractor
comparison extractor.xml @ 9:2b46c8d5952e draft
planemo upload for repository https://github.com/brsynth/icfree-ml commit 16315dee62caf50b1820964b0536c1cf61c67ceb
| author | tduigou |
|---|---|
| date | Fri, 07 Feb 2025 11:08:04 +0000 |
| parents | |
| children | 2580b6e8af84 |
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| 8:492e1736311c | 9:2b46c8d5952e |
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| 1 <tool id="icfree_extractor" name="iCFree extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT"> | |
| 2 <description>Process fluorescence data</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 cp '$initial_data_file' 'initial_data.csv' && | |
| 9 cp '$sampling_file' 'sampling.csv' && | |
| 10 python -m icfree.learner.extractor | |
| 11 --initial_data_file 'initial_data.csv' | |
| 12 --sampling_file 'sampling.csv' | |
| 13 --output_file 'extractor.csv' | |
| 14 #if str($adv.num_samples) != '' | |
| 15 --num_samples '$adv.num_samples' | |
| 16 #end if | |
| 17 #if str($adv.num_replicates) != '' | |
| 18 --num_replicates '$adv.num_replicates' | |
| 19 #end if | |
| 20 && | |
| 21 mv 'extractor.csv' '$output' | |
| 22 ]]></command> | |
| 23 <inputs> | |
| 24 <param name="initial_data_file" type="data" format="csv" label="FLuo/Lumi values"/> | |
| 25 <param name="sampling_file" type="data" format="csv" label="Sampling file"/> | |
| 26 <section name="adv" title="Advanced Options" expanded="false"> | |
| 27 <param argument="num_samples" type="integer" optional="true" label="Number of samples" /> | |
| 28 <param argument="num_replicates" type="integer" optional="true" label="Number of replicates" /> | |
| 29 </section> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data name="output" format="csv" label="${tool.name}" /> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test expect_num_outputs="1"> | |
| 36 <!-- python -m icfree.learner.extractor -initial_data_file extractor.input.initial_data.csv -sampling_file extractor.input.sampling.csv -output_file extractor.output.1.csv --> | |
| 37 <param name="initial_data_file" value="extractor.input.initial_data.csv" /> | |
| 38 <param name="sampling_file" value="extractor.input.sampling.csv" /> | |
| 39 <output name="output" ftype="csv"> | |
| 40 <assert_contents> | |
| 41 <has_n_lines n="58" /> | |
| 42 </assert_contents> | |
| 43 </output> | |
| 44 </test> | |
| 45 <test expect_num_outputs="1"> | |
| 46 <!-- python -m icfree.learner.extractor -initial_data_file extractor.input.initial_data.csv -sampling_file extractor.input.sampling.csv -output_file extractor.output.2.csv -num_samples 20 -num_replicates 3 --> | |
| 47 <param name="initial_data_file" value="extractor.input.initial_data.csv" /> | |
| 48 <param name="sampling_file" value="extractor.input.sampling.csv" /> | |
| 49 <param name="num_samples" value="20" /> | |
| 50 <param name="num_replicates" value="3" /> | |
| 51 <output name="output" ftype="csv"> | |
| 52 <assert_contents> | |
| 53 <has_n_lines n="21" /> | |
| 54 </assert_contents> | |
| 55 </output> | |
| 56 </test> | |
| 57 </tests> | |
| 58 <help><![CDATA[ | |
| 59 Extractor | |
| 60 ========== | |
| 61 Process fluoresence data | |
| 62 | |
| 63 ]]></help> | |
| 64 <expand macro="creator"/> | |
| 65 <expand macro="citation"/> | |
| 66 </tool> |