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comparison sccaf_macros.xml @ 0:95670267a5b6 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
author ebi-gxa
date Mon, 14 Oct 2019 08:10:33 -0400
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children 37a4c22f600b
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-1:000000000000 0:95670267a5b6
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">sccaf</requirement>
5 </requirements>
6 </xml>
7 <token name="@TOOL_VERSION@">0.0.7</token>
8 <token name="@SCCAF_INTRO@">
9 SCCAF explained
10 ===============
11
12 Single Cell Clustering Assessment Framework (SCCAF) is a novel method for
13 automated identification of putative cell types from single cell RNA-seq
14 (scRNA-seq) data. By iteratively applying clustering and a machine learning
15 approach to gene expression profiles of a given set of cells, SCCAF
16 simultaneously identifies distinct cell groups and a weighted list of feature
17 genes for each group. The feature genes, which are overexpressed in the
18 particular cell group, jointly discriminate the given cell group from other
19 cells. Each such group of cells corresponds to a putative cell type or state,
20 characterised by the feature genes as markers.
21 </token>
22 <token name="@HELP@">More information can be found at https://github.com/SCCAF/SCCAF</token>
23 <token name="@PLOT_OPTS@">
24 #if $do_plotting.plot
25 -P output.png
26 --projectio $do_plotting.projection
27 --components $do_plotting.components
28 #if $do_plotting.color_by
29 --color-by $do_plotting.color_by
30 #end if
31 #if $do_plotting.groups
32 --group $do_plotting.groups
33 #end if
34 #if $do_plotting.use_raw
35 --use-raw
36 #end if
37 #if $do_plotting.palette
38 --palette $do_plotting.palette
39 #end if
40 #if $do_plotting.show_edges
41 --edges
42 #end if
43 #if $do_plotting.show_arrows
44 --arrows
45 #end if
46 #if not $do_plotting.color_order
47 --no-sort-order
48 #end if
49 #if $do_plotting.omit_frame
50 --frameoff
51 #end if
52 #end if
53 </token>
54 <xml name="citations">
55 <citations>
56 <citation type="doi"></citation>
57 <citation type="bibtex">
58 @misc{githubsccaf,
59 author = {Miao, Zhichao},
60 year = {2018},
61 title = {SCCAF},
62 publisher = {GitHub},
63 journal = {GitHub repository},
64 url = {https://github.com/Functional-Genomics/SCCAF},
65 }</citation>
66 <yield />
67 </citations>
68 </xml>
69 <xml name="input_object_params">
70 <param name="input_obj_file" argument="--input-object-file" type="data" format="h5" label="Input object in AnnData hdf5 format" help="Normally the result of Scanpy (or equivalent), which already has both a visualisation (either tSNE, UMAP or PCA - needed) and clustering (ideally) pre-computed."/>
71 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
72 <option value="anndata" selected="true">AnnData format hdf5</option>
73 <option value="loom">Loom format hdf5, current support is incomplete</option>
74 </param>
75 </xml>
76 <xml name="output_object_params">
77 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
78 <option value="anndata" selected="true">AnnData format hdf5</option>
79 <option value="loom">Loom format hdf5, current support is defective</option>
80 </param>
81 </xml>
82 <xml name="output_plot_params">
83 <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/>
84 <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/>
85 <param name="projection" argument="--projection" type="select" label="Plot projection">
86 <option value="2d" selected="true">2D</option>
87 <option value="3d">3D</option>
88 </param>
89 <param name="components" argument="--components" type="text" value="1,2" label="Components to plot, comma separated integers"/>
90 <param name="palette" argument="--palette" type="text" optional="true" label="Palette"/>
91 <param name="use_raw" argument="--use-raw" type="boolean" checked="false" label="Use raw attributes if present"/>
92 <param name="show_edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
93 <param name="show_arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
94 <param name="color_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
95 <param name="omit_frame" argument="--frameoff" type="boolean" checked="false" label="Show frame"/>
96 </xml>
97 </macros>