Mercurial > repos > goeckslab > mesmer
comparison mesmer.xml @ 1:02abff468d60 draft
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
| author | goeckslab |
|---|---|
| date | Thu, 10 Nov 2022 20:38:34 +0000 |
| parents | 53240d7c1fc5 |
| children | 187918c47051 |
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| 0:53240d7c1fc5 | 1:02abff468d60 |
|---|---|
| 4 <macros> | 4 <macros> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 | 7 |
| 8 <expand macro="requirements"/> | 8 <expand macro="requirements"/> |
| 9 <expand macro="stdio"/> | |
| 9 <expand macro="version_cmd"/> | 10 <expand macro="version_cmd"/> |
| 10 | 11 |
| 11 <command detect_errors="exit_code"><![CDATA[ | 12 <command detect_errors="exit_code"><![CDATA[ |
| 12 ln -s '$nuclear_image' 'input.tif' && | 13 ln -s '$nuclear_image' 'input.tif' && |
| 13 @CMD_BEGIN@ | 14 @CMD_BEGIN@ |
| 51 </outputs> | 52 </outputs> |
| 52 <tests> | 53 <tests> |
| 53 <test> | 54 <test> |
| 54 <param name="nuclear_image" value="test.tiff" /> | 55 <param name="nuclear_image" value="test.tiff" /> |
| 55 <param name="compartment" value="nuclear" /> | 56 <param name="compartment" value="nuclear" /> |
| 56 <param name="membrane_select.membrane_segment" value="False" /> | 57 <param name="membrane_segment" value="False" /> |
| 57 <param name="image_mmp" value="0.65" /> | 58 <param name="image_mpp" value="0.65" /> |
| 58 <param name="squeeze" value="--squeeze" /> | 59 <param name="squeeze" value="--squeeze" /> |
| 59 <output name="mask" ftype="tiff"> | 60 <output name="mask" ftype="tiff"> |
| 60 <assert_contents> | 61 <assert_contents> |
| 61 <has_size value="360000" delta="1000" /> | 62 <has_size value="360000" delta="1000" /> |
| 62 </assert_contents> | 63 </assert_contents> |