Mercurial > repos > ebi-gxa > seurat_dim_plot

changeset 1:d539788175d4 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
author ebi-gxa
date Wed, 13 Mar 2019 12:53:31 -0400
parents 4f3a5ecefce5
children 4e73c73291cd
files seurat_dim_plot.xml seurat_macros.xml
diffstat 2 files changed, 35 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/seurat_dim_plot.xml	Mon Mar 04 12:18:09 2019 -0500
+++ b/seurat_dim_plot.xml	Wed Mar 13 12:53:31 2019 -0400
@@ -1,13 +1,13 @@
-<tool id="seurat_dim_plot" name="Plot dimension reduction" version="2.3.1+galaxy0">
-    <description>Graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</description>
+<tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="2.3.1+galaxy0">
+    <description>graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</description>
     <macros>
         <import>seurat_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="version" />
     <command detect_errors="exit_code"><![CDATA[
-        seurat-dim-plot.R 
-        --input-object-file '$input' 
+        seurat-dim-plot.R
+        --input-object-file '$input'
         #if $reduction_use
         --reduction-use '$reduction_use'
         #end if
@@ -58,18 +58,18 @@
         <param type="data" name="cells_use" format="tabular" label="Cells list" help='File to be used to derive a vector of cells to plot (default is all cells)' optional='true'/>
         <param type="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting' />
         <param type="float" name="label_size" value='4' label="Label size" help='Sets size of labels'/>
-        <param type="boolean" name="do_label" checked="false" label='Whether to label the clusters' truevalue="TRUE" falsevalue="FALSE" />
+        <param type="boolean" name="do_label" checked="false" label='Label clusters' truevalue="TRUE" falsevalue="FALSE" />
         <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways' />
         <param type="text" name="plot_title" format="text" label='Plot title' />
         <param type="boolean" name="do_bare" checked="false" label='Do only minimal formatting' truevalue="TRUE" falsevalue="FALSE" />
-        <param type="text" name="cols_use" format="text" label='Comma-separated list of colors, each color corresponds to an identity class. By default, ggplot assigns colors.' />
-        <param type="text" name="pt_shape" format="text" label='If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells.' />
-        <param type="boolean" name="coord_fixed" checked="false" label='Use a fixed scale coordinate system (for spatial coordinates). Default is FALSE.' truevalue="TRUE" falsevalue="FALSE" />
-        <param type="boolean" name="no_axes" checked="false" label='Setting to TRUE will remove the axes.' truevalue="TRUE" falsevalue="FALSE" />
+        <param type="text" name="cols_use" format="text" label="Colors" help='Comma-separated list of colors, each color corresponds to an identity class. By default, ggplot assigns colors.' />
+        <param type="text" name="pt_shape" format="text" label="Cell attribute for shape" help='If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells.' />
+        <param type="boolean" name="coord_fixed" checked="false" label="Fixed-scaled coordinate system" help='Use a fixed scale coordinate system (for spatial coordinates). Default is FALSE.' truevalue="TRUE" falsevalue="FALSE" />
+        <param type="boolean" name="no_axes" checked="false" label="Remove Axes" help='Setting to TRUE will remove the axes.' truevalue="TRUE" falsevalue="FALSE" />
         <param type="boolean" name="dark_theme" checked="false" label='Use a dark theme for the plot..' truevalue="TRUE" falsevalue="FALSE" />
-        <param type="text" name="plot_order" format="text" label='Comma-separated string specifying the order of plotting for the idents (clusters). This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top).' />
-        <param type="integer" name="png_width" value='1000' label='Width of png (px)' />
-        <param type="integer" name="png_height" value='1000' label='Height of png (px)'/>
+        <param type="text" name="plot_order" format="text" label="Ident (clusters) order" help='Comma-separated string specifying the order of plotting for the idents (clusters). This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top).' />
+        <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.' />
+        <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
     </inputs>
     <outputs>
         <data name="output_image_file" format="png" from_work_dir="pca.png" label="${tool.name} on ${on_string}"/>
@@ -77,8 +77,8 @@
     <tests>
         <test>
             <param name="input" value="seurat_clustered.rds" />
-            <output name="output_image_file" file="pca.png" />     
-        </test>    
+            <output name="output_image_file" file="pca.png" />
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
@@ -108,6 +108,7 @@
 .. _Seurat: https://www.nature.com/articles/nbt.4096
 .. _Satija Lab: https://satijalab.org/seurat/
 
+@VERSION_HISTORY@
 
     ]]></help>
     <expand macro="citations" />
--- a/seurat_macros.xml	Mon Mar 04 12:18:09 2019 -0500
+++ b/seurat_macros.xml	Wed Mar 13 12:53:31 2019 -0400
@@ -22,9 +22,29 @@
       <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
     </xml>
 
+    <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+
+0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9.
+
+2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
+EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(https://github.com/drosofff) and Lea Bellenger(https://github.com/bellenger-l).
+      ]]></token>
+
+
     <xml name="citations">
         <citations>
             <citation type="doi">10.1038/nbt.4096</citation>
+            <citation type="bibtex">
+              @misc{r-seurat-scripts.git,
+              author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
+              year = {2018},
+              title = {Seurat-scripts: command line interface for Seurat},
+              publisher = {GitHub},
+              journal = {GitHub repository},
+              url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
+            }
+            </citation>
         </citations>
     </xml>
 </macros>