| Previous changeset 0:ed1becc01910 (2017-03-04) Next changeset 2:635c90a27692 (2024-02-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21 |
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modified:
export2graphlan.xml |
| b |
| diff -r ed1becc01910 -r b16989c1e3a7 export2graphlan.xml --- a/export2graphlan.xml Sat Mar 04 11:44:38 2017 -0500 +++ b/export2graphlan.xml Wed Aug 07 14:49:12 2019 -0400 |
| [ |
| b'@@ -1,16 +1,17 @@\n-<tool id="export2graphlan" name="Export to GraPhlAn" version="0.19">\n- <description></description>\n+<tool id="export2graphlan" name="Export to GraPhlAn" version="@VERSION@+@GALAXY_VERSION@">\n+ <macros>\n+ <token name="@VERSION@">0.20</token>\n+ <token name="@GALAXY_VERSION@">galaxy0</token>\n+ </macros>\n <requirements>\n- <requirement type="package" version="0.19">export2graphlan</requirement>\n+ <requirement type="package" version="@VERSION@">export2graphlan</requirement>\n </requirements>\n- <stdio>\n- </stdio>\n <version_command>\n <![CDATA[\n-export2graphlan.py -v\n+export2graphlan.py -h | grep "ver."\n ]]>\n </version_command>\n- <command>\n+ <command detect_errors="exit_code">\n <![CDATA[\n export2graphlan.py\n --lefse_input \'$lefse_input\'\n@@ -19,62 +20,80 @@\n #end if\n -t \'$tree\'\n -a \'$annotation\'\n- #if $annotations\n- --annotations \'$annotations\'\n+ #if str($annotations) != \'\'\n+ --annotations $annotations\n #end if\n- #if $external_annotations\n- --external_annotations \'$external_annotations\'\n+ #if str($external_annotations) != \'\'\n+ --external_annotations $external_annotations\n #end if\n- #if $background_levels\n- --background_levels \'$background_levels\'\n+ #if str($background_levels) != \'\'\n+ --background_levels $background_levels\n #end if\n- #if $background_clades\n+ #if str($background_clades) != \'\'\n --background_clades \'$background_clades\'\n #end if\n- #if $background_colors\n+ #if str($background_colors) != \'\'\n --background_colors \'$background_colors\'\n #end if\n- #if $title\n+ #if str($title) != \'\'\n --title \'$title\'\n #end if\n-\n- --title_font_size \'$title_font_size\' \n- --def_clade_size \'$def_clade_size\'\n- --min_clade_size \'$min_clade_size\'\n- --max_clade_size \'$max_clade_size\'\n- --def_font_size \'$def_font_size\'\n- --min_font_size \'$min_font_size\'\n- --max_font_size \'$max_font_size\'\n- --annotation_legend_font_size \'$annotation_legend_font_size\'\n- --abundance_threshold \'$abundance_threshold\'\n-\n- #if $most_abundant\n- --most_abundant \'$most_abundant\'\n+ #if str($title_font_size) != \'\'\n+ --title_font_size $title_font_size\n+ #end if\n+ #if str($def_clade_size) != \'\' \n+ --def_clade_size $def_clade_size\n+ #end if\n+ #if str($min_clade_size) != \'\'\n+ --min_clade_size $min_clade_size\n+ #end if\n+ #if str($max_clade_size) != \'\'\n+ --max_clade_size $max_clade_size\n #end if\n- #if $least_biomarkers\n- --least_biomarkers \'$least_biomarkers\'\n+ #if str($def_font_size) != \'\'\n+ --def_font_size $def_font_size\n+ #end if\n+ #if str($min_font_size) != \'\'\n+ --min_font_size $min_font_size\n+ #end if\n+ #if str($max_font_size) != \'\'\n+ --max_font_size $max_font_size\n+ #end if\n+ #if str($annotation_legend_font_size) != \'\'\n+ --annotation_legend_font_size $annotation_legend_font_size\n+ #end if\n+ #if str($abundance_threshold) != \'\'\n+ --abundance_threshold $abundance_threshold\n #end if\n-\n- --fname_row \'$fname_row\'\n- --sname_row \'$sname_row\'\n-\n- #if $metadata_rows\n- --metadata_rows \'$metadata_rows\'\n+ #if str($most_abundant) != \'\'\n+ --most_abundant $most_abundant\n+ '..b'e="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"/>\n+ <param argument="--title" type="text" optional="True" label="Title of the GraPhlAn plot" />\n+ <param argument="--title_font_size" type="integer" optional="True" label="Title font size"/>\n+ <param argument="--def_clade_size" type="integer" optional="True" label="Default size for clades that are not found as biomarkers"/>\n+ <param argument="--min_clade_size" type="integer" optional="True" label="Minimum value of clades that are biomarkers"/>\n+ <param argument="--max_clade_size" type="integer" optional="True" label="Maximum value of clades that are biomarkers"/>\n+ <param argument="--def_font_size" type="integer" optional="True" label="Default font size"/>\n+ <param argument="--min_font_size" type="integer" optional="True" label="Minimum font size"/>\n+ <param argument="--max_font_size" type="integer" optional="True" label="Maximum font size"/>\n+ <param argument="--annotation_legend_font_size" type="integer" optional="True" label="Font size for the annotation legend"/>\n+ <param argument="--abundance_threshold" type="float" optional="True" label="Minimun abundance value for a clade to be annotated"/>\n+ <param argument="--most_abundant" type="integer" optional="True" label="Number of clades to highlight"/>\n+ <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"/>\n+ <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"/>\n+ <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"/>\n+ <param argument="--metadata_rows" type="integer" optional="True" label="Row number to use as metadata"/>\n+ <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"/>\n+ <param argument="--sperc" type="float" optional="True" label="Percentile of sample value distribution for sample selection"/>\n+ <param argument="--fperc" type="float" optional="True" label="Percentile of feature value distribution for sample selection"/>\n+ <param argument="--stop" type="integer" optional="True" label="Number of top samples to select" help="The order is based on percentile specified by --sperc"/>\n+ <param argument="--ftop" type="integer" optional="True" label="Number of top features to select" help="The order is based on percentile specified by --fperc"/>\n </inputs>\n <outputs>\n <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />\n@@ -139,16 +158,8 @@\n <param name="max_font_size" value="12"/>\n <param name="annotation_legend_font_size" value="10"/>\n <param name="abundance_threshold" value="20.0"/>\n- <param name="most_abundant" value=""/>\n- <param name="least_biomarkers" value=""/>\n <param name="fname_row" value="0"/>\n <param name="sname_row" value="0" />\n- <param name="metadata_rows" value=""/>\n- <param name="skip_rows" value=""/>\n- <param name="sperc" value=""/>\n- <param name="fperc" value=""/>\n- <param name="stop" value=""/>\n- <param name="ftop" value=""/>\n <output name="annotation" file="annotation_output.txt"/>\n <output name="tree" file="tree_output.txt"/>\n </test>\n' |