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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 1a2cbe050c6b172147064cb53b16d6833f138b68
author | iuc |
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date | Fri, 09 Feb 2024 21:29:27 +0000 |
parents | b16989c1e3a7 |
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<tool id="export2graphlan" name="Export to GraPhlAn" version="@VERSION@+@GALAXY_VERSION@"> <macros> <token name="@VERSION@">0.20</token> <token name="@GALAXY_VERSION@">galaxy0</token> </macros> <xrefs> <xref type="bio.tools">export2graphlan</xref> </xrefs> <requirements> <requirement type="package" version="@VERSION@">export2graphlan</requirement> </requirements> <version_command> <![CDATA[ export2graphlan.py -h | grep "ver." ]]> </version_command> <command detect_errors="exit_code"> <![CDATA[ export2graphlan.py --lefse_input '$lefse_input' #if $input_lefse_output.input_lefse_output_test == "true" --lefse_output '$input_lefse_output.lefse_output' #end if -t '$tree' -a '$annotation' #if str($annotations) != '' --annotations $annotations #end if #if str($external_annotations) != '' --external_annotations $external_annotations #end if #if str($background_levels) != '' --background_levels $background_levels #end if #if str($background_clades) != '' --background_clades '$background_clades' #end if #if str($background_colors) != '' --background_colors '$background_colors' #end if #if str($title) != '' --title '$title' #end if #if str($title_font_size) != '' --title_font_size $title_font_size #end if #if str($def_clade_size) != '' --def_clade_size $def_clade_size #end if #if str($min_clade_size) != '' --min_clade_size $min_clade_size #end if #if str($max_clade_size) != '' --max_clade_size $max_clade_size #end if #if str($def_font_size) != '' --def_font_size $def_font_size #end if #if str($min_font_size) != '' --min_font_size $min_font_size #end if #if str($max_font_size) != '' --max_font_size $max_font_size #end if #if str($annotation_legend_font_size) != '' --annotation_legend_font_size $annotation_legend_font_size #end if #if str($abundance_threshold) != '' --abundance_threshold $abundance_threshold #end if #if str($most_abundant) != '' --most_abundant $most_abundant #end if #if str($least_biomarkers) != '' --least_biomarkers $least_biomarkers #end if #if str($title_font_size) != '' --fname_row $fname_row #end if #if str($title_font_size) != '' --sname_row $sname_row #end if #if str($metadata_rows) != '' --metadata_rows $metadata_rows #end if #if str($skip_rows) != '' --skip_rows $skip_rows #end if #if str($sperc) != '' --sperc $sperc #end if #if str($fperc) != '' --fperc $fperc #end if #if str($stop) != '' --stop $stop #end if #if str($ftop) != '' --ftop $ftop #end if ]]> </command> <inputs> <param argument="--lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file"/> <conditional name="input_lefse_output"> <param name="input_lefse_output_test" type="select" label="Use a LEfSe output file as input?" help=""> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <param argument="--lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file"/> </when> <when value="false"/> </conditional> <param argument="--annotations" type="text" optional="True" label="List which levels should be annotated in the tree" help="The levels must be in comma-separated form"/> <param argument="--external_annotations" type="text" optional="True" label="List which levels should use the external legend for the annotation" help="The levels must be in comma-separated form"/> <param argument="--background_levels" type="text" optional="True" label="List which levels should be highlight with a shaded background" help="The levels must be in comma-separated form"/> <param argument="--background_clades" type="text" optional="True" label="List of the clades that should be highlight with a shaded background" help="The clades must be in comma-separated form"/> <param argument="--background_colors" type="text" optional="True" label="List of color to use for the shaded background" help="Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()). The different colors must be in comma-separated form"/> <param argument="--title" type="text" optional="True" label="Title of the GraPhlAn plot" /> <param argument="--title_font_size" type="integer" optional="True" label="Title font size"/> <param argument="--def_clade_size" type="integer" optional="True" label="Default size for clades that are not found as biomarkers"/> <param argument="--min_clade_size" type="integer" optional="True" label="Minimum value of clades that are biomarkers"/> <param argument="--max_clade_size" type="integer" optional="True" label="Maximum value of clades that are biomarkers"/> <param argument="--def_font_size" type="integer" optional="True" label="Default font size"/> <param argument="--min_font_size" type="integer" optional="True" label="Minimum font size"/> <param argument="--max_font_size" type="integer" optional="True" label="Maximum font size"/> <param argument="--annotation_legend_font_size" type="integer" optional="True" label="Font size for the annotation legend"/> <param argument="--abundance_threshold" type="float" optional="True" label="Minimun abundance value for a clade to be annotated"/> <param argument="--most_abundant" type="integer" optional="True" label="Number of clades to highlight"/> <param argument="--least_biomarkers" type="integer" optional="True" label="Minimum number of biomarkers to extract" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers"/> <param argument="--fname_row" type="integer" optional="True" label="Row number containing the names of the features" help="-1 specifies that no names are present in the matrix"/> <param argument="--sname_row" type="integer" optional="True" label="Row number containing the names of the samples" help="-1 specifies that no names are present in the matrix"/> <param argument="--metadata_rows" type="integer" optional="True" label="Row number to use as metadata"/> <param argument="--skip_rows" type="text" optional="True" label="Row number to skip from the input file" help="The row numbers are indexed to 0 and comma separated"/> <param argument="--sperc" type="float" optional="True" label="Percentile of sample value distribution for sample selection"/> <param argument="--fperc" type="float" optional="True" label="Percentile of feature value distribution for sample selection"/> <param argument="--stop" type="integer" optional="True" label="Number of top samples to select" help="The order is based on percentile specified by --sperc"/> <param argument="--ftop" type="integer" optional="True" label="Number of top features to select" help="The order is based on percentile specified by --fperc"/> </inputs> <outputs> <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" /> <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" /> </outputs> <tests> <test> <param name="lefse_input" value="input_profile.tabular"/> <param name="input_lefse_output_test" value="no" /> <param name="annotations" value=""/> <param name="external_annotations" value=""/> <param name="background_levels" value=""/> <param name="background_clades" value=""/> <param name="background_colors" value=""/> <param name="title" value=""/> <param name="title_font_size" value="15"/> <param name="def_clade_size" value="10"/> <param name="min_clade_size" value="20"/> <param name="max_clade_size" value="200"/> <param name="def_font_size" value="10"/> <param name="min_font_size" value="8"/> <param name="max_font_size" value="12"/> <param name="annotation_legend_font_size" value="10"/> <param name="abundance_threshold" value="20.0"/> <param name="fname_row" value="0"/> <param name="sname_row" value="0" /> <output name="annotation" file="annotation_output.txt"/> <output name="tree" file="tree_output.txt"/> </test> </tests> <help><![CDATA[ **What it does** export2graphlan is a conversion software tool to produce both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. For more information, check the `user manual <https://github.com/SegataLab/export2graphlan/>`_. ]]></help> <citations> <citation type="doi">10.7717/peerj.1029</citation> </citations> </tool>