Mercurial > repos > bebatut > graphlan
changeset 0:c5746c07ca5e draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
| author | bebatut |
|---|---|
| date | Mon, 01 Feb 2016 07:45:14 -0500 |
| parents | |
| children | 5cdaa98d9376 |
| files | graphlan.xml graphlan_annotate.xml tool_dependencies.xml |
| diffstat | 3 files changed, 214 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/graphlan.xml Mon Feb 01 07:45:14 2016 -0500 @@ -0,0 +1,118 @@ +<tool id="graphlan" name="GraPhlAn" version="0.1.0"> + + <description>to produce graphical output of an input tree</description> + + <requirements> + <requirement type="package" version="1.66">biopython</requirement> + <requirement type="package" version="1.4">matplotlib</requirement> + <requirement type="package" version="1.0">graphlan</requirement> + </requirements> + + <stdio> + </stdio> + + <version_command> +<![CDATA[ +python \${GRAPHLAN_DIR}/graphlan.py -v +]]> + </version_command> + + <command> +<![CDATA[ + python \${GRAPHLAN_DIR}/graphlan.py + --format $format + + #if $dpi + --dpi $dpi + #end if + + --size $size + + #if $pad + --pad $pad + #end if + + $input_tree + + #if str($format) == "png" + $png_output_image + #else if str($format) == "pdf" + $pdf_output_image + #else if str($format) == "ps" + $ps_output_image + #else if str($format) == "eps" + $eps_output_image + #else + $svg_output_image + #end if +]]> + </command> + + <inputs> + <param name="input_tree" type="data" format="txt" label="Input tree in + PhlyloXML format" help=""/> + + <param name='format' type="select" label="Output format" + help="(--format)"> + <option value="png" selected="true">PNG</option> + <option value="pdf">PDF</option> + <option value="ps">PS</option> + <option value="eps">EPS</option> + <option value="svg">SVG</option> + </param> + + <param name="dpi" type="integer" label="Dpi of the output image + (Optional)" help="For non vectorial formats (--dpi)" optional="True"/> + + <param name="size" type="integer" value="7" label="Size of the output image + (in inches)" help="(--size)"/> + + <param name="pad" type="integer" label="Distance between the most external + graphical element and the border of the image (Optional)" + help="(--pad)" optional="True"/> + </inputs> + + <outputs> + <data format="png" name="png_output_image" + label="${tool.name} on ${on_string}: Image"> + <filter>format=="png"</filter> + </data> + <data format="pdf" name="pdf_output_image" + label="${tool.name} on ${on_string}: Image"> + <filter>format=="pdf"</filter> + </data> + <data format="ps" name="ps_output_image" + label="${tool.name} on ${on_string}: Image"> + <filter>format=="ps"</filter> + </data> + <data format="eps" name="eps_output_image" + label="${tool.name} on ${on_string}: Image"> + <filter>format=="eps"</filter> + </data> + <data format="svg" name="svg_output_image" + label="${tool.name} on ${on_string}: Image"> + <filter>format=="svg"</filter> + </data> + </outputs> + + <tests> + <test> + </test> + </tests> + + <help><![CDATA[ + +**What it does** + +GraPhlAn is a software tool for producing high-quality circular +representations of taxonomic and phylogenetic trees. GraPhlAn focuses on +concise, integrative, informative, and publication-ready representations of +phylogenetically- and taxonomically-driven investigation. + +For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_. + + ]]></help> + + <citations> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/graphlan_annotate.xml Mon Feb 01 07:45:14 2016 -0500 @@ -0,0 +1,69 @@ +<tool id="graphlan_annotate" name="Modify an input tree for GraPhlAn" version="0.1.0"> + + <description></description> + + <requirements> + <requirement type="package" version="1.66">biopython</requirement> + <requirement type="package" version="1.4">matplotlib</requirement> + <requirement type="package" version="1.0">graphlan</requirement> + </requirements> + + <stdio> + </stdio> + + <version_command> +<![CDATA[ +python \${GRAPHLAN_DIR}/graphlan_annotate.py -v +]]> + </version_command> + + <command> +<![CDATA[ + python \${GRAPHLAN_DIR}/graphlan_annotate.py + #if $annot + --annot $annot + #end if + + $input_tree + $output_tree +]]> + </command> + + <inputs> + <param name="input_tree" type="data" format="txt" label="Input tree" + help="Newick, Nexus, PhyloXML or plain text"/> + + <param name="annot" type="data" format="txt" label="Annotation file + (Optional)" help="(--annot)" optional="True"/> + </inputs> + + <outputs> + <data format="text" name="output_tree" + label="${tool.name} on ${on_string}: Tree in PhyloXML" /> + </outputs> + + <tests> + <test> + </test> + </tests> + + <help><![CDATA[ + +**What it does** + +GraPhlAn is a software tool for producing high-quality circular +representations of taxonomic and phylogenetic trees. GraPhlAn focuses on +concise, integrative, informative, and publication-ready representations of +phylogenetically- and taxonomically-driven investigation. + +`graphlan_annotate` modifies any input tree (in any of the three standard format) +adding additional information regarding structural or graphical aspects of the tree +(like colors and style of the taxa, labels, shadows, heatmaps, ...). + +For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_. + + ]]></help> + + <citations> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Feb 01 07:45:14 2016 -0500 @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="biopython" version="1.66"> + <repository changeset_revision="907c57486667" name="package_python_2_7_biopython_1_66" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="matplotlib" version="1.4"> + <repository changeset_revision="9a4214646e88" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="graphlan" version="1.0"> + <install version="1.0"> + <actions> + <action type="shell_command"> + hg clone https://hg@bitbucket.org/nsegata/graphlan + </action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="set_to" name="GRAPHLAN_DIR">$INSTALL_DIR/</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme /> + </package> +</tool_dependency>