| Next changeset 1:9f23fe0cb70b (2022-10-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d |
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added:
snipit.xml test-data/input.fasta test-data/snp_plot.jpg test-data/snp_plot.pdf test-data/snp_plot.png test-data/snp_plot_ex.png |
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| diff -r 000000000000 -r 20b4c59bec12 snipit.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snipit.xml Sun Jul 17 15:01:31 2022 +0000 |
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| @@ -0,0 +1,123 @@ +<tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0"> + <description>Summarise snps relative to a reference sequence</description> + <macros> + <token name="@TOOL_VERSION@">1.0.5</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">snipit</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + snipit '$alignment' + #if $opt.reference + -r '$opt.reference' + #end if + #if $opt.labels + -l '$opt.labels' + #end if + --l-header '$opt.l_header' + -f '$opt.format' + --height '$opt.height' + --width '$opt.width' + --size-option '$opt.size_option' + $opt.flip_vertical + #if $opt.exclude_positions + --exclude-positions '$opt.exclude_positions' + #end if + $opt.exclude_ambig_pos + $opt.sort_by_mutation_number + $opt.sort_by_id + #if $opt.sort_by_mutations + --sort-by-mutations '$opt.sort_by_mutations' + #end if + $opt.high_to_low + -c '$opt.colour_palette' + ]]> </command> + <inputs> + <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" /> + <section name="opt" title="Optional arguments" expanded="true"> + <param name="reference" argument="-r" type="text" optional="true" label="Reference sequence (by sequence ID)" help="Indicates which sequence in the alignment is the reference (by sequence ID). Default: first sequence in alignment" /> + <param name="labels" argument="-l" type="data" format="csv" optional="true" label="Labels" help="Optional csv file of labels to show in output snipit plot. Default: sequence names"/> + <param argument="--l-header" type="text" value="name,label" label="Label headers" help="Comma separated string of column headers in label csv. First field indicates sequence name column, second the label column. Default: 'name,label'" /> + <param name="format" argument="-f" type="select" value="png" label="Output file format" help="Format options. Default: png"> + <option value="png" selected="true">png</option> + <option value="jpg">jpg</option> + <option value="pdf">pdf</option> + <option value="svg">svg</option> + <option value="tiff">tiff</option> + </param> + <param argument="--height" type="float" value="0.0" label="Figure height" help="Overwrite the default figure height." /> + <param argument="--width" type="float" value="0.0" label="Figure width" help="Overwrite the default figure width." /> + <param argument="--size-option" type="select" value="scale" label="Sizing options" help="Specify options for sizing. Options: expand, scale"> + <option value="expand">expand</option> + <option value="scale" selected="true">scale</option> + </param> + <param argument="--flip-vertical" type="boolean" truevalue="--flip-vertical" falsevalue="" value="false" label="Flip plot orientation?" help="Flip the orientation of the plot so sequences are below the reference rather than above it. Default: false" /> + <param argument="--exclude-positions" type="text" optional="true" label="Excluded positions" help="One or more range (closed, inclusive; one-indexed) or specific position to exclude in the output. Ex. '100-150' or Ex. '100 101' Considered after '--include-positions'." /> + <param argument="--exclude-ambig-pos" type="boolean" truevalue="--exclude-ambig-pos" falsevalue="" value="false" label="Exclude ambig positions?" help="Exclude positions with ambig base in any sequences. Considered after '--include-positions'" /> + <param argument="--sort-by-mutation-number" type="boolean" truevalue="--sort-by-mutation-number" falsevalue="" value="false" label="Sort by mutation number?" help="Render the graph with sequences sorted by the number of SNPs relative to the reference (fewest to most). Default: False" /> + <param argument="--sort-by-id" type="boolean" truevalue="--sort-by-id" falsevalue="" value="false" label="Sort by sequence ID?" help="Sort sequences alphabetically by sequence id. Default: False" /> + <param argument="--sort-by-mutations" type="text" optional="true" label="Sort by mutations" help="Sort sequences by bases at specified positions. Positions are comma separated integers. Ex. '1,2,3'" /> + <param argument="--high-to-low" type="boolean" truevalue="--high-to-low" falsevalue="" value="false" label="Sort high to low?" help="If 'sort by mutation number' is selected, show the sequences with the fewest SNPs closest to the reference. Default: False" /> + <param name="colour_palette" argument="-c" type="select" value="classic" label="Colour palette" help="Specify colour palette. Options: primary, classic, purine-pyrimidine, greyscale, wes, verity"> + <option value="primary">primary</option> + <option value="classic" selected="true">classic</option> + <option value="purine-pyrimidine">purine-pyrimidine</option> + <option value="greyscale">greyscale</option> + <option value="wes">wes</option> + <option value="verity">verity</option> + </param> + </section> + </inputs> + <outputs> + <data name="snp_plot" format="png" label="snp plot" from_work_dir="snp_plot.*"> + <change_format> + <when input="opt.format" value="jpg" format="jpg" /> + <when input="opt.format" value="pdf" format="pdf" /> + <when input="opt.format" value="svg" format="svg" /> + <when input="opt.format" value="tiff" format="tiff" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="alignment" value="input.fasta" /> + <output name="snp_plot" ftype="png" file="snp_plot.png" compare="sim_size"/> + </test> + <test> + <param name="alignment" value="input.fasta" /> + <param name="reference" value="USA_2" /> + <param name="format" value="pdf" /> + <param name="flip_vertical" value="true" /> + <output name="snp_plot" ftype="pdf" file="snp_plot.pdf" compare="sim_size" /> + </test> + <test> + <param name="alignment" value="input.fasta" /> + <param name="format" value="jpg" /> + <param name="colour_palette" value="verity" /> + <output name="snp_plot" ftype="jpg" file="snp_plot.jpg" /> + </test> + <test> + <param name="alignment" value="input.fasta" /> + <param name="excluded_positions" value="1-100" /> + <param name="exclude_ambig_pos" value="true" /> + <param name="high_to_low" value="true" /> + <output name="snp_plot" ftype="png" file="snp_plot_ex.png" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Snipit finds the SNPs relative to a reference in a multiple sequence alignment and highlights these changes as a figure. + ]]> + </help> + <citations> + <citation type="bibtex"> + @UNPUBLISHED{OToole2017, + author = {O'Toole, Aine}, + title = {snipit: Summarise snps relative to your reference sequence.}, + year = {2017}, + url = {https://github.com/aineniamh/snipit} + } + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 20b4c59bec12 test-data/input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fasta Sun Jul 17 15:01:31 2022 +0000 |
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