WIP: Add trimal #6397
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WIP: Add trimal #6397
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bgruening
reviewed
Oct 3, 2024
| long_description: trimAl is a tool for the automated removal of spurious sequences | ||
| or poorly aligned regions from a multiple sequence alignment. | ||
| name: trimal | ||
| owner: padge |
| @@ -0,0 +1,159 @@ | |||
| <tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.00" python_template_version="3.5"> | |||
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| <tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.00" python_template_version="3.5"> | |
| <tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> |
| @@ -0,0 +1,159 @@ | |||
| <tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.00" python_template_version="3.5"> | |||
| <description>A tool for automated alignment trimming</description> | |||
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| <description>A tool for automated alignment trimming</description> | |
| <description>for automated alignment trimming</description> |
| <requirement type="package" version="@TOOL_VERSION@">trimal</requirement> | ||
| </requirements> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| trimal -in $input1 -out $trimmed_output -htmlout $html_summary ${out_format_selector} |
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| trimal -in $input1 -out $trimmed_output -htmlout $html_summary ${out_format_selector} | |
| trimal -in '$in' -out '$trimmed_output' -htmlout '$html_summary' ${out_format_selector} |
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| ]]></command> | ||
| <inputs> | ||
| <param name="input1" type="data" format="fasta,clustal,pir,phylip,nexus,mega" multiple="false" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" optional="false" /> |
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| <param name="input1" type="data" format="fasta,clustal,pir,phylip,nexus,mega" multiple="false" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" optional="false" /> | |
| <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" /> |
| <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="similarity threshold" help="Minimum average similarity allowed. Range: [0 - 1]" multiple="false"/> | ||
| <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="min conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve." multiple="false"/> | ||
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| </when> |
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| </when> | |
| </when> | |
| <when value="-nogaps"/> |
and the others need to be added
| <data name="html_summary" format="html" label="trimal html summary."/> | ||
| </outputs> | ||
| <tests> | ||
| <test> |
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please add expected_num_outputs
| <when input="out_format_selector" value="-phylip3.2" format="phylip" /> | ||
| <when input="out_format_selector" value="-phylip3.2_m10" format="phylip" /> | ||
| <when input="out_format_selector" value="-clustal" format="clustal" /> | ||
| <when input="out_format_selector" value="-mega" format="mega" /> |
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does the mega format exists in Galaxy?
| </test> | ||
| </tests> | ||
| <help><
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FOR CONTRIBUTOR:
This is a collaboration together with @pauldg and @nicodr97. @pauldg made the original wrapper, that resides at https://github.com/usegalaxy-be/galaxytools/tree/main/trimal.
What I changed so far:
phylip3.2_m10) so changed to a simpler definition list. I didn't manage to escape or cheese the strict formatting rules.Planemo lintnow only fails on '<when /> block' not being present at the 'Conditional [trimming_mode]'. Could you add them @nicodr97 or @pauldg as was done at the 'custom' value?WIP will be removed after these changes and IUC's checklist have been addressed.
Would also like to point out that Trimal 1.5.0 exists, but think we should get 1.4.1 wrapper properly finished and then release a new updated wrapper for the 1.5.0 version.