Mercurial > repos > gaelcge > r_signac_galaxy
comparison signac_dimplot.xml @ 0:6e0b320d8b6a draft default tip
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
| author | gaelcge |
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| date | Tue, 02 Aug 2022 19:11:27 +0000 |
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| -1:000000000000 | 0:6e0b320d8b6a |
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| 1 <tool id="signac_dimplot" name="Plot dimensional reduction" version="0.1.0" python_template_version="3.5"> | |
| 2 <description> of your cell embeddings.</description> | |
| 3 <macros> | |
| 4 <import>signac_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <stdio> | |
| 8 <exit_code range="1:"/> | |
| 9 </stdio> | |
| 10 <command><![CDATA[ | |
| 11 Rscript '${__tool_directory__}'/signac-dimplot.R --signac-object $signac_object --dims $dims --pt-size $pt_size --label-size $label_size --group-by $group_by --png-width $png_width --png-height $png_height --output_image_file $dimplot_file | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/> | |
| 15 <param type="text" name="dims" value='1,2' label="Dimensions to use." help='Dimension to use.'/> | |
| 16 <param type="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting'/> | |
| 17 <param type="float" name="label_size" value='4' label="Label size" help='Sets size of labels'/> | |
| 18 <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways'/> | |
| 19 <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.'/> | |
| 20 <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data name="dimplot_file" format="png" from_work_dir="Dimplot.png" label="Signac.dimplot.png"/> | |
| 24 </outputs> | |
| 25 <help><![CDATA[ | |
| 26 This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object. | |
| 27 ]]></help> | |
| 28 </tool> |