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annotate macros.xml @ 4:2675ff99a53b draft default tip

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 130ef7e8ae6cab35866b72617e53d35acc11475a
author goeckslab
date Wed, 28 Feb 2024 20:52:00 +0000
parents c60b810d570d
children
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53240d7c1fc5 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 5fb6aa9066c68d9972b3cc4be13503a952f952a5
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1 <?xml version="1.0"?>
53240d7c1fc5 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 5fb6aa9066c68d9972b3cc4be13503a952f952a5
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <container type="docker">quay.io/goeckslab/deepcell:@TOOL_VERSION@</container>
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6 </requirements>
53240d7c1fc5 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 5fb6aa9066c68d9972b3cc4be13503a952f952a5
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7 </xml>
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8 <xml name="stdio">
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9 <stdio>
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10 <regex match="MemoryError"
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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11 source="both"
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12 level="fatal_oom"
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13 description="Out of Memory" />
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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14 <regex match="std::bad_alloc"
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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15 source="both"
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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16 level="fatal_oom"
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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17 description="Out of Memory" />
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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18 <regex match="java.lang.OutOfMemoryError"
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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19 source="both"
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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20 level="fatal_oom"
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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21 description="Out of Memory" />
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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22 <regex match="Out of memory"
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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23 source="both"
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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24 level="fatal_oom"
02abff468d60 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
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25 description="Out of Memory" />
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26 </stdio>
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27 </xml>
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29 <xml name="watershed_adv_options">
187918c47051 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 40737a3341bb2352f4f8560889bb53362fd624be
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30 <param name="maxima_smooth" type="integer" value="0" label="Maxima Smooth"/>
187918c47051 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 40737a3341bb2352f4f8560889bb53362fd624be
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31 <param name="interior_threshold" type="float" value="0.2" label="Interior Threshold"/>
187918c47051 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 40737a3341bb2352f4f8560889bb53362fd624be
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32 <param name="interior_smooth" type="integer" value="2" label="Interior Smooth"/>
187918c47051 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 40737a3341bb2352f4f8560889bb53362fd624be
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33 <param name="small_objects_threshold" type="integer" value="15" label="Small Objects Threshold"/>
187918c47051 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 40737a3341bb2352f4f8560889bb53362fd624be
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34 <param name="fill_holes_threshold" type="integer" value="15" label="Fill Holes Threshold"/>
187918c47051 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 40737a3341bb2352f4f8560889bb53362fd624be
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35 <param name="radius" type="integer" value="1" label="Radius"/>
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36 </xml>
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38 <xml name="nuclear_options_macro">
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39 <section name="nuclear_options" title="Nuclear Options" expanded="true">
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40 <param name="pixel_expansion" type="integer" optional="true" label="Number of pixels to expand nucleus"/>
187918c47051 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 40737a3341bb2352f4f8560889bb53362fd624be
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41 <param name="maxima_threshold" type="float" value="0.1" label="Maxima Threshold"/>
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42 <section name="adv_options" title="Advanced Nuclear Options" expanded="false">
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43 <expand macro="watershed_adv_options"/>
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44 </section>
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45 </section>
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46 </xml>
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47
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48 <xml name="wc_options_macro">
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49 <section name="wc_options" title="Whole Cell Options" expanded="true">
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50 <param name="wc_channels" type="text" value="1" label="The numerical indices of the channel(s) for the membrane markers" help="No quotes, separated by comma. e.g. 0, 1."/>
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51 <param name="maxima_threshold" type="float" value="0.075" label="Maxima Threshold"/>
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52 <section name="adv_options" title="Advanced Whole Cell Options" expanded="false">
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53 <expand macro="watershed_adv_options"/>
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54 </section>
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55 </section>
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56 </xml>
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57
0
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58 <xml name="citations">
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59 <citations>
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60 <citation type="doi">10.1038/s41587-021-01094-0</citation>
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61 </citations>
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62 </xml>
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63
2
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64 <token name="@TOOL_VERSION@">0.12.3</token>
3
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65 <token name="@VERSION_SUFFIX@">3</token>
0
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66 </macros>