Mercurial > repos > ebi-gxa > anndata_ops

comparison scanpy_macros2.xml @ 19:53a251c6d991 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/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
author ebi-gxa
date Wed, 05 May 2021 12:15:47 +0000
parents e4bb4666449e
children 890fb06a2893
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18:e4bb4666449e 19:53a251c6d991
28 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. 28 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
29 ]]></token> 29 ]]></token>
30 <token name="@INPUT_OPTS@"> 30 <token name="@INPUT_OPTS@">
31 --input-format '${input_format}' input.h5 31 --input-format '${input_format}' input.h5
32 </token> 32 </token>
33 <token name="@SAVE_MATRIX_OPTS@">
34 #if $save_raw
35 --save-raw
36 #end if
37 #if $save_layer
38 --save-layer ${settings.save_layer}
39 #end if
40 </token>
33 <token name="@OUTPUT_OPTS@"> 41 <token name="@OUTPUT_OPTS@">
34 #if str($output_format).startswith('anndata') 42 #if str($output_format).startswith('anndata')
35 --show-obj stdout --output-format anndata output.h5 43 --show-obj stdout --output-format anndata output.h5
36 #else 44 #else
37 --show-obj stdout --output-format loom output.h5 45 --show-obj stdout --output-format loom output.h5
49 </token> 57 </token>
50 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token> 58 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
51 59
52 <xml name="requirements"> 60 <xml name="requirements">
53 <requirements> 61 <requirements>
54 <requirement type="package" version="0.3.3">scanpy-scripts</requirement> 62 <requirement type="package" version="0.4.0">scanpy-scripts</requirement>
55 <yield/> 63 <yield/>
56 </requirements> 64 </requirements>
57 </xml> 65 </xml>
58 66
59 <xml name="citations"> 67 <xml name="citations">
120 <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom"> 128 <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
121 <filter>output_format == 'loom'</filter> 129 <filter>output_format == 'loom'</filter>
122 </data> 130 </data>
123 </xml> 131 </xml>
124 132
133 <xml name="save_matrix_params">
134 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="false"
135 label="Save adata to adata.raw before processing?" />
136 <param name="save_layer" argument="--save-layer" type="text" optional="true"
137 label="Save adata.X to the specified layer before processing."/>
138 </xml>
139
125 <xml name="output_plot_params"> 140 <xml name="output_plot_params">
126 <param name="fig_title" argument="--title" type="text" label="Figure title"/> 141 <param name="fig_title" argument="--title" type="text" label="Figure title"/>
127 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/> 142 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
128 <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/> 143 <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
129 <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/> 144 <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>