Mercurial > repos > ebi-gxa > sccaf_regress_out
comparison sccaf_macros.xml @ 1:5ef0610e9f50 draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
author | ebi-gxa |
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date | Mon, 25 Nov 2019 06:28:23 -0500 |
parents | 885db50f1bc1 |
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0:885db50f1bc1 | 1:5ef0610e9f50 |
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2 <xml name="requirements"> | 2 <xml name="requirements"> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="@TOOL_VERSION@">sccaf</requirement> | 4 <requirement type="package" version="@TOOL_VERSION@">sccaf</requirement> |
5 </requirements> | 5 </requirements> |
6 </xml> | 6 </xml> |
7 <token name="@TOOL_VERSION@">0.0.8</token> | 7 <token name="@TOOL_VERSION@">0.0.9</token> |
8 <token name="@SCCAF_INTRO@"> | 8 <token name="@SCCAF_INTRO@"> |
9 SCCAF explained | 9 SCCAF explained |
10 =============== | 10 =============== |
11 | 11 |
12 Single Cell Clustering Assessment Framework (SCCAF) is a novel method for | 12 Single Cell Clustering Assessment Framework (SCCAF) is a novel method for |
65 }</citation> | 65 }</citation> |
66 <yield /> | 66 <yield /> |
67 </citations> | 67 </citations> |
68 </xml> | 68 </xml> |
69 <xml name="input_object_params"> | 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."/> | 70 <param name="input_obj_file" argument="--input-object-file" type="data" format="h5,h5ad" 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> | 71 </xml> |
76 <xml name="output_object_params"> | 72 <xml name="output_object_params"> |
77 <param name="output_format" argument="--output-format" type="select" label="Format of output object"> | 73 <param name="output_format" argument="--output-format" type="select" label="Format of output object"> |
78 <option value="anndata" selected="true">AnnData format hdf5</option> | 74 <option value="anndata_h5ad" selected="true">AnnData format hdf5</option> |
79 <option value="loom">Loom format hdf5, current support is defective</option> | 75 <option value="anndata">AnnData format (h5 for older versions)</option> |
80 </param> | 76 </param> |
77 </xml> | |
78 <xml name="output_data_obj" token_description="operation"> | |
79 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> | |
80 <filter>output_format == 'anndata_h5ad'</filter> | |
81 </data> | |
82 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> | |
83 <filter>output_format == 'anndata'</filter> | |
84 </data> | |
81 </xml> | 85 </xml> |
82 <xml name="output_plot_params"> | 86 <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"/> | 87 <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"/> | 88 <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"> | 89 <param name="projection" argument="--projection" type="select" label="Plot projection"> |