| Previous changeset 0:53240d7c1fc5 (2022-09-08) Next changeset 2:187918c47051 (2022-12-28) |
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Commit message:
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371 |
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modified:
macros.xml mesmer.xml |
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| diff -r 53240d7c1fc5 -r 02abff468d60 macros.xml --- a/macros.xml Thu Sep 08 15:17:30 2022 +0000 +++ b/macros.xml Thu Nov 10 20:38:34 2022 +0000 |
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| @@ -5,7 +5,26 @@ <container type="docker">quay.io/goeckslab/mesmer:@TOOL_VERSION@</container> </requirements> </xml> - + <xml name="stdio"> + <stdio> + <regex match="MemoryError" + source="both" + level="fatal_oom" + description="Out of Memory" /> + <regex match="std::bad_alloc" + source="both" + level="fatal_oom" + description="Out of Memory" /> + <regex match="java.lang.OutOfMemoryError" + source="both" + level="fatal_oom" + description="Out of Memory" /> + <regex match="Out of memory" + source="both" + level="fatal_oom" + description="Out of Memory" /> + </stdio> + </xml> <xml name="version_cmd"> <version_command>@CMD_BEGIN@ --help</version_command> </xml> @@ -16,6 +35,6 @@ </xml> <token name="@TOOL_VERSION@">0.3.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@CMD_BEGIN@">python /usr/src/app/run_app.py mesmer</token> </macros> |
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| diff -r 53240d7c1fc5 -r 02abff468d60 mesmer.xml --- a/mesmer.xml Thu Sep 08 15:17:30 2022 +0000 +++ b/mesmer.xml Thu Nov 10 20:38:34 2022 +0000 |
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| @@ -6,6 +6,7 @@ </macros> <expand macro="requirements"/> + <expand macro="stdio"/> <expand macro="version_cmd"/> <command detect_errors="exit_code"><![CDATA[ @@ -53,8 +54,8 @@ <test> <param name="nuclear_image" value="test.tiff" /> <param name="compartment" value="nuclear" /> - <param name="membrane_select.membrane_segment" value="False" /> - <param name="image_mmp" value="0.65" /> + <param name="membrane_segment" value="False" /> + <param name="image_mpp" value="0.65" /> <param name="squeeze" value="--squeeze" /> <output name="mask" ftype="tiff"> <assert_contents> |