add enzyme list to morpheus tool #766
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bgruening
reviewed
Jul 12, 2024
tools/morpheus/morpheus.xml
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| @@ -1,49 +1,11 @@ | |||
| <tool id="morpheus" name="Morpheus" version="2.255.0"> | |||
| <tool id="morpheusid" name="Morpheus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |||
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please don't change the tool ID, otherwise we loose the tool lineage
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My bad. I forgot to change it back after testing.
tools/morpheus/macros.xml
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| @@ -0,0 +1,77 @@ | |||
| <macros> | |||
| <token name="@TOOL_VERSION@">2.255.0</token> | |||
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the version needs to be bumped
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agreed! The latest version is 288. do you want me to bump it up to 288?
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@bgruening I bumped the version up to 288 from 255 and updated the output of the test section. Can you check again.
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Please also see the failing lint:
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bgruening
reviewed
Jul 15, 2024
| @@ -150,7 +112,10 @@ | |||
| #if str($vm) != 'None': | |||
| #set $vmods = str($vm).replace(',',';') | |||
| -vm="$vmods" | |||
| #end if | |||
| #end if | |||
| #if str($p) != 'None': | |||
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It can never be None, because the select param is not optional.
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FOR CONTRIBUTOR:
[x]I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
[x]License permits unrestricted use (educational + commercial)
[x]This PR adds a new tool or tool collection
[x]This PR updates an existing tool or tool collection
[]This PR does something else (explain below)
Background:
The morpheus wrapper does not have the parameter (p) which allows user to select enzyme to be used in the morpheus search process. The option p is listed in https://cwenger.github.io/Morpheus/args.html .
In addition to include the p option in the wrapper. I have tidied up the morpheus wrapper by creating a macro file for tool version , tokens, values and enzyme list for the paramters used in the wrapper.