Mercurial > repos > bebatut > export2graphlan
changeset 1:d7cf3b50a074 draft default tip
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 3472a70f35769aaeafa40e8fbce97aac2c4ea4f8-dirty
| author | bebatut |
|---|---|
| date | Tue, 21 Jun 2016 08:05:01 -0400 |
| parents | b344522045f3 |
| children | |
| files | export2graphlan.xml tool_dependencies.xml |
| diffstat | 2 files changed, 28 insertions(+), 39 deletions(-) [+] |
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--- a/export2graphlan.xml Wed Apr 20 06:09:29 2016 -0400 +++ b/export2graphlan.xml Tue Jun 21 08:05:01 2016 -0400 @@ -19,12 +19,12 @@ </version_command> <command> -<![CDATA[ +<![CDATA[ export2graphlan.py -i $lefse_input - #if $lefse_output - -o lefse_output + #if $input_lefse_output.input_lefse_output_test == "true" + -o $input_lefse_output.lefse_output #end if -t $tree @@ -49,13 +49,13 @@ #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 + + --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 @@ -78,8 +78,8 @@ #if $metadata_rows --metadata_rows $metadata_rows #end if - - #if $skip_rows + + #if $skip_rows --skip_rows $skip_rows #end if @@ -104,7 +104,17 @@ <inputs> <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/> - <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/> + <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 name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file" help="(--lefse_output)"/> + </when> + <when value="false"/> + </conditional> <param name="annotations" type="text" label="List which levels should be annotated in the tree (Optional)" help="The levels must be in comma-separated form (--annotations)" optional="True"/> @@ -115,47 +125,28 @@ <param name="background_clades" type="text" label="List of the clades that should be highlight with a shaded background (Optional)" help="The clades must be in comma-separated form (--background_clades)" optional="True"/> <param name="background_colors" type="text" label="List of color to use for the shaded background (Optional)" 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 (--background_colors)" optional="True"/> - + <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)" help="(--title)" optional="True"/> - <param name="title_font_size" type="integer" value="15" label="Title font size" help="(--title_font_size)"/> - <param name="def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers" help="(--def_clade_size)"/> - <param name="min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers" help="(--min_clade_size)"/> - <param name="max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers" help="(--max_clade_size)"/> - <param name="def_font_size" type="integer" value="10" label="Default font size" help="(--def_font_size)"/> - <param name="min_font_size" type="integer" value="8" label="Minimum font size" help="(--min_font_size)"/> - <param name="max_font_size" type="integer" value="12" label="Maximum font size" help="(--max_font_size)"/> - <param name="annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend" help="(--annotation_legend_font_size)"/> - <param name="abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated" help="(--abundance_threshold)"/> - <param name="most_abundant" type="integer" label="Number of clades to highlight (Optional)" help="(--most_abundant)" optional="True"/> <param name="least_biomarkers" type="integer" label="Minimum number of biomarkers to extract (Optional)" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers(--least_biomarkers)" optional="True"/> <param name="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 (--fname_row)"/> - <param name="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 (--sname_row)"/> - <param name="metadata_rows" type="integer" label="Row number to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/> - <param name="skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers ar indexed to 0 and comma separated (--skip_rows)" optional="True"/> - - <param name="sperc" type="float" label="Percentile of sample value - distribution for sample selection (Optional)" help="(--sperc)" - optional="True"/> - + <param name="sperc" type="float" label="Percentile of sample value distribution for sample selection (Optional)" help="(--sperc)" optional="True"/> <param name="fperc" type="float" label="Percentile of feature value distribution for sample selection (Optional)" help="(--fperc)" optional="True"/> - <param name="stop" type="integer" label="Number of top samples to select (Optional)" help="The order is based on percentile specified by --sperc (--stop)" optional="True"/> - <param name="ftop" type="integer" label="Number of top features to select (Optional)" help="The order is based on percentile specified by --fperc (--ftop)" optional="True"/> </inputs> @@ -167,6 +158,7 @@ <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=""/> @@ -198,18 +190,15 @@ </tests> <help><![CDATA[ - **What it does** -export2graphlan is a conversion software tool for producing 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. +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 -For more information, check the -`user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_. +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> \ No newline at end of file +</tool>
--- a/tool_dependencies.xml Wed Apr 20 06:09:29 2016 -0400 +++ b/tool_dependencies.xml Tue Jun 21 08:05:01 2016 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="pandas" version="0.16"> - <repository changeset_revision="ea929a7f2976" name="package_python_2_7_pandas_0_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="2511234c20da" name="package_python_2_7_pandas_0_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="scipy" version="0.16"> <repository changeset_revision="80f8536c6dc2" name="package_python_2_7_scipy_0_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />