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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1570f3a28232b4b88385cdfbb68f79d80ff1dabb |
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modified:
macros.xml mafft-add.xml mafft.xml |
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| diff -r a65296ffb4a0 -r 6f28e90db932 macros.xml --- a/macros.xml Fri Sep 30 19:24:47 2022 +0000 +++ b/macros.xml Tue Oct 31 15:48:53 2023 +0000 |
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| @@ -1,7 +1,13 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">0</token> <token name="@TOOL_VERSION@">7.508</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">22.01</token> + <xml name="biotools"> + <xrefs> + <xref type="bio.tools">MAFFT</xref> + </xrefs> + </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">mafft</requirement> |
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| diff -r a65296ffb4a0 -r 6f28e90db932 mafft-add.xml --- a/mafft-add.xml Fri Sep 30 19:24:47 2022 +0000 +++ b/mafft-add.xml Tue Oct 31 15:48:53 2023 +0000 |
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| @@ -1,10 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION@"> +<tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Align a sequence,alignment or fragments to an existing alignment.</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="biotools"/> + <expand macro="requirements"/> <stdio> <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> |
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| diff -r a65296ffb4a0 -r 6f28e90db932 mafft.xml --- a/mafft.xml Fri Sep 30 19:24:47 2022 +0000 +++ b/mafft.xml Tue Oct 31 15:48:53 2023 +0000 |
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| @@ -1,9 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION@"> - <description>Multiple alignment program for amino acid or nucleotide sequences</description> +<tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> +<description>Multiple alignment program for amino acid or nucleotide sequences</description> <macros> <import>macros.xml</import> </macros> + <expand macro="biotools"/> <expand macro="requirements" /> <stdio> <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> @@ -229,32 +230,51 @@ <param name="outputFormat" value="--clustalout"/> <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln" lines_diff="2" /> </test> + <!-- WARNING: the results of the following test depends on #threads. + The result seems deterministic for single threaded execution, i.e. GALAXY_SLOTS=1 planemo test + However, GH CI/CD uses 2 threads and results vary --> <test expect_num_outputs="1" > <param name="inputSequences" value="sample.fa"/> <param name="flavourType" value="custom"/> - <param name="matrix_condition" value="BLOSUM"/> + <conditional name="matrix_condition"> + <param name="matrix" value="BLOSUM"/> + </conditional> <param name="BLOSUM" value="62"/> <param name="distance_method" value="--fastapair"/> <param name="weighti" value="2.7"/> <param name="iterations" value="1000"/> <param name="outputFormat" value="--clustalout"/> - <output name="outputAlignment" ftype="clustal" file="mafft_custom_result.aln" lines_diff="2" /> + <output name="outputAlignment" ftype="clustal" file="mafft_custom_result.aln" compare="sim_size"> + <assert_contents> + <has_n_lines n="458" delta="0"/> + <has_text text="CLUSTAL format alignment by MAFFT F-INS-i"/> + <has_text text="NPIVYGISHPKY"/> + <has_text text="1=="/> + <has_text text="36=="/> + <has_line line="8=opsin, ------------------------------------------------------------"/> + </assert_contents> + </output> </test> </tests> <help> <![CDATA[ **What it does** + MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. - From the MAFFT man page, an overview of the different predefined flavours of the tool. + From the MAFFT man page, an overview of the different predefined flavours of the tool is as follows: + **Accuracy-oriented methods:** + - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information): - mafft --localpair --maxiterate 1000 input [> output] - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information): - mafft --globalpair --maxiterate 1000 input [> output] - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences): - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps. + **Speed-oriented methods:** + - FFT-NS-i (iterative refinement method; two cycles only): - mafft --retree 2 --maxiterate 2 input [> output] - FFT-NS-i (iterative refinement method; max. 1000 iterations): @@ -271,23 +291,14 @@ - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output] **Options:** - --auto - Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2) - --adjustdirection - Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored. - --op - Gap opening penalty, default: 1.53 - --ep - Offset (works like gap extension penalty), default: 0.0 - --maxiterate - Maximum number of iterative refinement, default: 0 - --clustalout - Output: clustal format, default: fasta - --thread - Number of threads (if unsure, --thread -1) - --retree number - Guide tree is built number times in the progressive stage. - Valid with 6mer distance. Default: 2 + + - --auto Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2) + - --adjustdirection Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored. + - --op Gap opening penalty, default: 1.53 + - --ep Offset (works like gap extension penalty), default: 0.0 + - --maxiterate Maximum number of iterative refinement, default: 0 + - --clustalout Output: clustal format, default: fasta + - --retree number Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2 ]]> </help> <expand macro="citations" /> |