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Updating Galaxy wrapper
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‎galaxy/honto.xml

Lines changed: 97 additions & 43 deletions
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@@ -50,16 +50,14 @@
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#end if
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#end if
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#if $heatmap.customize == "true":
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--cmap $heatmap.cmap
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--vmin $heatmap.vmin
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--vmax $heatmap.vmax
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--center $heatmap.center
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#if $heatmap.cbar == "yes":
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--cbar
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#end if
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--cmap $heatmap.cmap
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--vmin $heatmap.vmin
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--vmax $heatmap.vmax
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--center $heatmap.center
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#if $heatmap.cbar == "yes":
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--cbar
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#end if
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--nproc "\${GALAXY_SLOTS:-4}"
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--overwrite
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--verbose
@@ -90,7 +88,7 @@
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<conditional name="log_transform">
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<!-- Enable log-transformation -->
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<param name="enable_lt" type="boolean" checked="false" truevalue="yes" falsevalue="no"
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label="Log-transform z-scores?" />
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label="Log-transform z-scores" />
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<when value="yes">
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<!-- Scale options -->
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</conditional>
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</when>
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</conditional>
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<!-- Heatmap customization options -->
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<section name="heatmap" expanded="true"
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title="Heatmap customization"
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help="Access advanced options to customize the produced heatmap by specifying the colormap, scale, and color bar">
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<!-- Colormap -->
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<param name="cmap" type="text" value="PiYG"
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label="Heatmap colormap" />
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<!-- Log-transformation options -->
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<conditional name="heatmap">
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<!-- Enable log-transformation -->
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<param name="customize" type="boolean" checked="false" truevalue="true" falsevalue="false"
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label="Customize heatmap"
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help="Access advanced options to customize the graphical output." />
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<!-- Vmin -->
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<param name="vmin" type="float" value="2.2967"
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label="Select a vmin value"
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help="Min value to anchor the colormap" />
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<!-- In case of "true" -->
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<when value="true">
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<!-- Colormap -->
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<param name="cmap" type="text" value="PiYG"
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label="Heatmap colormap" />
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<!-- Vmin -->
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<param name="vmin" type="float" value="2.2967"
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label="Select a vmin value"
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help="Min value to anchor the colormap" />
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<!-- Vmax -->
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<param name="vmax" type="float" value="4.3957"
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label="Select a vmax value"
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help="Max value to anchor the colormap" />
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<!-- Center -->
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<param name="center" type="float" value="2.9957"
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label="Select a center"
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help="The value at which to center the colormap when plotting divergent data" />
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<!-- Cbar -->
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<param name="cbar" type="boolean" checked="false" truevalue="yes" falsevalue="no"
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label="Add a color bar" />
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</when>
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</conditional>
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<!-- Vmax -->
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<param name="vmax" type="float" value="4.3957"
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label="Select a vmax value"
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help="Max value to anchor the colormap" />
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<!-- Center -->
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<param name="center" type="float" value="2.9957"
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label="Select a center"
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help="The value at which to center the colormap when plotting divergent data" />
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<!-- Cbar -->
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<param name="cbar" type="boolean" checked="false" truevalue="yes" falsevalue="no"
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label="Add a color bar" />
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</section>
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</inputs>
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<outputs>
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</outputs>
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<help><![CDATA[
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Define the tool help here with info about input and output
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**Homophily Network Tool**
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`honto` is a tool designed for assessing and measuring homophily in networks whose nodes have categorical attributes,
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namely when the nodes of networks come partitioned into classes.
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Homophily evaluation is performed through the comparison between the relative edge density of the subgraphs,
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induced by each class, and the corresponding expected relative edge density under a null model.
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The novelty of our approach consists in prescribing an endogenous null model, namely, the sample space of the null model
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is built on the input network itself. This allows us to give exact explicit expressions for the z-scores of the
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relative edge density of each class as well as other related statistics
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-----
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**Input**
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The first input is file representing an undirected network composed by a list of edges like the example below.
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No header lines are allowed.
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+--------+--------+
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| TP0001 | TP1015 |
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+--------+--------+
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| TP0001 | TP0949 |
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+--------+--------+
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| TP0001 | TP0692 |
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+--------+--------+
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| ... | ... |
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+--------+--------+
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| TP0976 | TP0977 |
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+--------+--------+
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| TP1032 | TP1033 |
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+--------+--------+
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Please note that the above mentioned file could also have an additional column with numeric weight values.
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You may want to avoid considering some nodes by applying a threshold on this column.
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The second input is the nodes definition file. It contains a row for each node in the network with two columns
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with a mapping between the node name and a color or group id, like in the example below.
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No header lines are allowed in this case either.
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+--------+-----+
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| TP0001 | L |
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+--------+-----+
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| TP1015 | K |
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+--------+-----+
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| TP0949 | U |
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+--------+-----+
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| TP0692 | L |
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+--------+-----+
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| ... | ... |
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+--------+-----+
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| TP1032 | X |
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+--------+-----+
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| TP1033 | X |
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+--------+-----+
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-----
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**Output**
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The tool produces three output files. Two of them contains the z-scores for both edges and singletons.
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The third output is a PDF with the final heatmap.
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-----
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