Mercurial > repos > iuc > export2graphlan
diff export2graphlan.xml @ 0:ed1becc01910 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
author | iuc |
---|---|
date | Sat, 04 Mar 2017 11:44:38 -0500 |
parents | |
children | b16989c1e3a7 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/export2graphlan.xml Sat Mar 04 11:44:38 2017 -0500 @@ -0,0 +1,169 @@ +<tool id="export2graphlan" name="Export to GraPhlAn" version="0.19"> + <description></description> + <requirements> + <requirement type="package" version="0.19">export2graphlan</requirement> + </requirements> + <stdio> + </stdio> + <version_command> +<![CDATA[ +export2graphlan.py -v +]]> + </version_command> + <command> +<![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 $annotations + --annotations '$annotations' + #end if + #if $external_annotations + --external_annotations '$external_annotations' + #end if + #if $background_levels + --background_levels '$background_levels' + #end if + #if $background_clades + --background_clades '$background_clades' + #end if + #if $background_colors + --background_colors '$background_colors' + #end if + #if $title + --title '$title' + #end if + + --title_font_size '$title_font_size' + --def_clade_size '$def_clade_size' + --min_clade_size '$min_clade_size' + --max_clade_size '$max_clade_size' + --def_font_size '$def_font_size' + --min_font_size '$min_font_size' + --max_font_size '$max_font_size' + --annotation_legend_font_size '$annotation_legend_font_size' + --abundance_threshold '$abundance_threshold' + + #if $most_abundant + --most_abundant '$most_abundant' + #end if + #if $least_biomarkers + --least_biomarkers '$least_biomarkers' + #end if + + --fname_row '$fname_row' + --sname_row '$sname_row' + + #if $metadata_rows + --metadata_rows '$metadata_rows' + #end if + #if $skip_rows + --skip_rows '$skip_rows' + #end if + #if $sperc + --sperc '$sperc' + #end if + #if $fperc + --fperc '$fperc' + #end if + #if $stop + --stop '$stop' + #end if + #if $ftop + --ftop '$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" label="List which levels should be annotated in the tree" help="The levels must be in comma-separated form" optional="True"/> + <param argument="--external_annotations" type="text" label="List which levels should use the external legend for the annotation" help="The levels must be in comma-separated form" optional="True"/> + <param argument="--background_levels" type="text" label="List which levels should be highlight with a shaded background" help="The levels must be in comma-separated form" optional="True"/> + <param argument="--background_clades" type="text" label="List of the clades that should be highlight with a shaded background" help="The clades must be in comma-separated form" optional="True"/> + <param argument="--background_colors" type="text" 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" optional="True"/> + <param argument="--title" type="text" label="Title of the GraPhlAn plot" optional="True"/> + <param argument="--title_font_size" type="integer" value="15" label="Title font size"/> + <param argument="--def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers"/> + <param argument="--min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers"/> + <param argument="--max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers"/> + <param argument="--def_font_size" type="integer" value="10" label="Default font size"/> + <param argument="--min_font_size" type="integer" value="8" label="Minimum font size"/> + <param argument="--max_font_size" type="integer" value="12" label="Maximum font size"/> + <param argument="--annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend"/> + <param argument="--abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated"/> + <param argument="--most_abundant" type="integer" label="Number of clades to highlight" optional="True"/> + <param argument="--least_biomarkers" type="integer" 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" optional="True"/> + <param argument="--fname_row" type="integer" value="0" 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" value="0" 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" label="Row number to use as metadata" optional="True"/> + <param argument="--skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers are indexed to 0 and comma separated" optional="True"/> + <param argument="--sperc" type="float" label="Percentile of sample value distribution for sample selection" optional="True"/> + <param argument="--fperc" type="float" label="Percentile of feature value distribution for sample selection" optional="True"/> + <param argument="--stop" type="integer" label="Number of top samples to select" help="The order is based on percentile specified by --sperc" optional="True"/> + <param argument="--ftop" type="integer" label="Number of top features to select" help="The order is based on percentile specified by --fperc" optional="True"/> + </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="most_abundant" value=""/> + <param name="least_biomarkers" value=""/> + <param name="fname_row" value="0"/> + <param name="sname_row" value="0" /> + <param name="metadata_rows" value=""/> + <param name="skip_rows" value=""/> + <param name="sperc" value=""/> + <param name="fperc" value=""/> + <param name="stop" value=""/> + <param name="ftop" value=""/> + <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://bitbucket.org/CibioCM/export2graphlan/overview/>`_. + + ]]></help> + <citations> + </citations> +</tool>