Mercurial > repos > ebi-gxa > run_sccaf

comparison sccaf_macros.xml @ 1:647d34f125bc draft default tip

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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 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
author ebi-gxa
date Mon, 25 Nov 2019 06:28:58 -0500
parents ca26d4b4b02c
children
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0:ca26d4b4b02c 1:647d34f125bc
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@">0.0.7</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">