Mercurial > repos > iuc > export2graphlan
changeset 1:b16989c1e3a7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
| author | iuc |
|---|---|
| date | Wed, 07 Aug 2019 14:49:12 -0400 |
| parents | ed1becc01910 |
| children | 635c90a27692 |
| files | export2graphlan.xml |
| diffstat | 1 files changed, 91 insertions(+), 80 deletions(-) [+] |
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--- a/export2graphlan.xml Sat Mar 04 11:44:38 2017 -0500 +++ b/export2graphlan.xml Wed Aug 07 14:49:12 2019 -0400 @@ -1,16 +1,17 @@ -<tool id="export2graphlan" name="Export to GraPhlAn" version="0.19"> - <description></description> +<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> <requirements> - <requirement type="package" version="0.19">export2graphlan</requirement> + <requirement type="package" version="@VERSION@">export2graphlan</requirement> </requirements> - <stdio> - </stdio> <version_command> <![CDATA[ -export2graphlan.py -v +export2graphlan.py -h | grep "ver." ]]> </version_command> - <command> + <command detect_errors="exit_code"> <![CDATA[ export2graphlan.py --lefse_input '$lefse_input' @@ -19,62 +20,80 @@ #end if -t '$tree' -a '$annotation' - #if $annotations - --annotations '$annotations' + #if str($annotations) != '' + --annotations $annotations #end if - #if $external_annotations - --external_annotations '$external_annotations' + #if str($external_annotations) != '' + --external_annotations $external_annotations #end if - #if $background_levels - --background_levels '$background_levels' + #if str($background_levels) != '' + --background_levels $background_levels #end if - #if $background_clades + #if str($background_clades) != '' --background_clades '$background_clades' #end if - #if $background_colors + #if str($background_colors) != '' --background_colors '$background_colors' #end if - #if $title + #if str($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' + #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 $least_biomarkers - --least_biomarkers '$least_biomarkers' + #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 $abundance_threshold #end if - - --fname_row '$fname_row' - --sname_row '$sname_row' - - #if $metadata_rows - --metadata_rows '$metadata_rows' + #if str($most_abundant) != '' + --most_abundant $most_abundant + #end if + #if str($least_biomarkers) != '' + --least_biomarkers $least_biomarkers #end if - #if $skip_rows - --skip_rows '$skip_rows' + #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 $sperc - --sperc '$sperc' + #if str($skip_rows) != '' + --skip_rows $skip_rows #end if - #if $fperc - --fperc '$fperc' + #if str($sperc) != '' + --sperc $sperc #end if - #if $stop - --stop '$stop' + #if str($fperc) != '' + --fperc $fperc #end if - #if $ftop - --ftop '$ftop' + #if str($stop) != '' + --stop $stop + #end if + #if str($ftop) != '' + --ftop $ftop #end if ]]> </command> @@ -90,31 +109,31 @@ </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"/> + <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" /> @@ -139,16 +158,8 @@ <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>