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comparison macros.xml @ 0:8b9b8d358883 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/liana commit 8dc656081d3147b402485bd25affe05a22e5194e
author iuc
date Tue, 10 Mar 2026 13:41:01 +0000
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-1:000000000000 0:8b9b8d358883
1 <macros>
2 <token name="@TOOL_VERSION@">1.7.1</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">25.0</token>
5 <xml name="requirements">
6 <requirements>
7 <!-- Pin the version of anndata and pandas to avoid breaks in saving the h5ad macros -->
8 <requirement type="package" version="@TOOL_VERSION@">liana</requirement>
9 <requirement type="package" version="0.10.7">anndata</requirement>
10 <requirement type="package" version="1.9.6">scanpy</requirement>
11 <requirement type="package" version="2.1.4">pandas</requirement>
12 </requirements>
13 </xml>
14 <xml name="bio_tools">
15 <xrefs>
16 <xref type="bio.tools">liana</xref>
17 </xrefs>
18 </xml>
19 <xml name="creators">
20 <creator>
21 <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" />
22 <person givenName="Katarzyna" familyName="Kamieniecka" url="https://github.com/kkamieniecka" />
23 <person givenName="Pavankumar" familyName="Videm" url="https://github.com/pavanvidem" />
24 <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" />
25 <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" />
26 </creator>
27 </xml>
28 <xml name="citations">
29 <citations>
30 <citation type="doi">10.1038/s41556-024-01469-w</citation>
31 </citations>
32 </xml>
33
34 <!-- param macros -->
35 <xml name="sanitize_query" token_validinitial="string.printable">
36 <sanitizer>
37 <valid initial="@VALIDINITIAL@">
38 <remove value="&apos;"/>
39 </valid>
40 </sanitizer>
41 </xml>
42 <xml name="inputs_anndata">
43 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
44 </xml>
45 <xml name="inputs_common_advanced">
46 <section name="advanced_common" title="Advanced Options" expanded="false">
47 <param name="show_log" type="boolean" checked="false" label="Output Log?"/>
48 </section>
49 </xml>
50 <xml name="anndata_outputs">
51 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
52 </data>
53 <data name="hidden_output" format="txt" label="Log file" >
54 <filter>advanced_common['show_log']</filter>
55 </data>
56 </xml>
57
58 <!-- Liana-specific parameter macros -->
59 <xml name="param_groupby">
60 <param argument="groupby" type="text" value="" optional="false" label="Group By" help="Key to be used for grouping">
61 <expand macro="sanitize_query"/>
62 <validator type="empty_field" message="Please provide a valid groupby key (required)"/>
63 </param>
64 </xml>
65 <!-- Simple resource name parameter -->
66 <xml name="param_resource_name">
67 <param argument="resource_name" type="select" label="Ligand-receptor database" help="Built-in database of ligand-receptor pair annotations">
68 <option value="consensus" selected="true">consensus - Combined databases (recommended)</option>
69 <option value="cellchatdb">CellChat database</option>
70 <option value="cellphonedb">CellPhoneDB database</option>
71 <option value="connectomedb2020">Connectome database</option>
72 <option value="baccin2019">Baccin et al. 2019</option>
73 <option value="cellcall">CellCall</option>
74 <option value="cellinker">CellInker</option>
75 <option value="celltalkdb">CellTalkDB</option>
76 <option value="embrace">EMBRACE</option>
77 <option value="guide2pharma">Guide to Pharmacology</option>
78 <option value="hpmr">Human Protein-Protein Interactions</option>
79 <option value="icellnet">iCellNet</option>
80 <option value="italk">iTALK</option>
81 <option value="kirouac2010">Kirouac et al. 2010</option>
82 <option value="lrdb">LRDB</option>
83 <option value="mouseconsensus">mouseconsensus - Mouse data</option>
84 <option value="ramilowski2015">Ramilowski et al. 2015</option>
85 </param>
86 </xml>
87 <!-- Resource selection with hierarchy: interactions > resource > resource_name -->
88 <xml name="param_return_all_lrs">
89 <param argument="return_all_lrs" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Return all interactions" help="If enabled: include all L-R pairs from database even if they fail expression filter. If disabled: return only pairs meeting expr_prop threshold."/>
90 </xml>
91 <xml name="param_key_added">
92 <param argument="key_added" type="text" value="liana_res" label="Results key in adata.uns" help="Key in adata.uns where results will be stored. Default: 'liana_res'.">
93 <expand macro="sanitize_query"/>
94 </param>
95 </xml>
96 <xml name="param_use_raw">
97 <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use raw counts" help="If enabled: use adata.raw.X (raw/unprocessed counts). If disabled: use adata.X (processed/normalized expression). Default: enabled."/>
98 </xml>
99 <xml name="param_layer">
100 <param argument="layer" type="text" value="" optional="true" label="Layer in adata" help="Specific layer in adata.layers to use (e.g., 'log1p', 'scaled', 'raw'). If empty: uses adata.X.">
101 <expand macro="sanitize_query"/>
102 </param>
103 </xml>
104 <xml name="param_de_method">
105 <param argument="de_method" type="select" label="Differential expression test" help="Statistical method for rank_genes_groups (1-vs-Rest). t-test: parametric; wilcoxon: non-parametric, robust; logreg: logistic regression. Default: t-test.">
106 <option value="t-test" selected="true">t-test (default)</option>
107 <option value="t-test_overestim_var">t-test with variance correction</option>
108 <option value="wilcoxon">Wilcoxon rank-sum (non-parametric)</option>
109 <option value="logreg">Logistic regression</option>
110 </param>
111 </xml>
112 <xml name="param_n_perms">
113 <param argument="n_perms" type="integer" value="1000" min="0" optional="true" label="Permutation test iterations" help="Number of random permutations for statistical significance (CellPhoneDB, etc.). Default: 1000. Set to 0 to skip permutation testing."/>
114 </xml>
115 <xml name="param_seed">
116 <param argument="seed" type="integer" value="1337" label="Random seed for reproducibility" help=""/>
117 </xml>
118 <xml name="param_base">
119 <param argument="base" type="float" value="2.718281828459045" optional="true" label="Log transformation base" help="Base for reversing log-transformation of expression values. Default: e (2.718). Use 2 for log2 or 10 for log10 data."/>
120 </xml>
121 <xml name="param_supp_columns">
122 <param argument="supp_columns" type="text" value="" optional="true" label="Additional columns to be added" help="From any of the methods implemented in liana , or any of the columns returned by scanpy, each starting with ligand_* or receptor_*. For example, ['ligand_pvals', 'receptor_pvals']"/>
123 </xml>
124
125 <!-- Grouped parameter macros for cleaner code -->
126 <xml name="params_common_basic">
127 <expand macro="param_groupby"/>
128 <expand macro="param_resource_selection"/>
129 <param argument="expr_prop" type="float" value="0.1" min="0" max="1" label="Minimum expression proportion" help="Minimum expression proportion for the ligands and receptors (+ their subunits) in the corresponding cell identities. Set to 0 to return unfiltered results"/>
130 <param argument="min_cells" type="integer" value="5" min="1" label="Minimum cells" help="Minimum number of cells per cell identity to be considered for downstream analysis. Default: 5."/>
131 </xml>
132 <xml name="params_common_output">
133 <expand macro="param_return_all_lrs"/>
134 <expand macro="param_key_added"/>
135 <expand macro="param_layer"/>
136 </xml>
137 <!-- Combined common params for methods without permutations -->
138 <xml name="params_lr_method_basic">
139 <expand macro="params_common_basic"/>
140 <expand macro="params_common_output"/>
141 <expand macro="param_supp_columns"/>
142 <expand macro="param_de_method"/>
143 <expand macro="param_seed"/>
144 </xml>
145 <!-- Combined common params for methods with permutations -->
146 <xml name="params_lr_method_with_perms">
147 <expand macro="params_common_basic"/>
148 <expand macro="params_common_output"/>
149 <expand macro="param_supp_columns"/>
150 <expand macro="param_de_method"/>
151 <expand macro="param_n_perms"/>
152 <expand macro="param_seed"/>
153 </xml>
154
155 <!-- Spatial-specific parameter macros -->
156 <xml name="param_spatial_key">
157 <param argument="spatial_key" type="text" value="spatial" label="Spatial coordinates key" help="The key in adata.obsm where the spatial coordinates are stored">
158 <expand macro="sanitize_query"/>
159 </param>
160 </xml>
161 <xml name="param_nz_threshold">
162 <param argument="nz_threshold" type="float" value="0.1" min="0" max="1" label="Non-zero threshold for views" help=""/>
163 </xml>
164 <xml name="param_set_diag">
165 <param argument="set_diag" type="boolean" truevalue="True" falsevalue="False" checked="true" label=" Set the diagonal of the connectivity matrix to 1" help=""/>
166 </xml>
167 <xml name="param_kernel">
168 <param argument="kernel" type="select" label="Radial basis function kernel" value="@DEFAULT_KERNEL@" help="Used for the generation of the connectivity matrix for the paraview">
169 <option value="misty_rbf">misty_rbf - MISTy RBF (default)</option>
170 <option value="gaussian">gaussian - Gaussian kernel</option>
171 <option value="exponential">exponential - Exponential decay</option>
172 <option value="linear">linear - Inverse distance</option>
173 </param>
174 </xml>
175 <xml name="param_bandwidth">
176 <param argument="bandwidth" type="float" value="100" min="0" label="Kernel bandwidth" help=""/>
177 </xml>
178 <xml name="param_zoi">
179 <param argument="zoi" type="float" value="0" min="0" label="Kernel Zone of indifference" help=""/>
180 </xml>
181 <xml name="param_cutoff">
182 <param argument="cutoff" type="float" value="0.1" min="0" max="1" label="Connectivity matrix cutoff" help=""/>
183 </xml>
184 <xml name="param_model">
185 <param argument="model" type="select" label="MISTy prediction model" help="Statistical model for feature importance ranking">
186 <option value="RandomForestModel" selected="true">RandomForestModel (default)</option>
187 <option value="LinearModel">LinearModel</option>
188 <option value="RobustLinearModel">RobustLinearModel</option>
189 </param>
190 </xml>
191 <xml name="param_bypass_intra">
192 <param argument="bypass_intra" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Exclude intra-view from training" help=""/>
193 </xml>
194 <xml name="param_resource_selection">
195 <conditional name="resource_selection">
196 <param name="resource_type" type="select" label="Interaction source" help="Priority: interactions list > custom file > built-in database. Choose based on whether you have custom L-R pairs or want to use pre-defined resources.">
197 <option value="resource_name" selected="true">Use built-in database</option>
198 <option value="resource">Upload custom resource file</option>
199 <option value="interactions">Enter specific interaction pairs</option>
200 </param>
201 <when value="resource_name">
202 <conditional name="resource_api_cached">
203 <param name="resource_source_selector" type="select" label="Resource source" help="Use cached resources from this Galaxy server (installed via Data Manager) for fast offline access, or download from LIANA API.">
204 <option value="builtin">Download from LIANA API</option>
205 <option value="cached" selected="true">Cached on server (from Data Manager)</option>
206 </param>
207 <when value="cached">
208 <param name="resource_cached" type="select" label="Ligand-receptor database (cached)" help="Select from resources installed by the LIANA Resources Data Manager.">
209 <options from_data_table="liana_resources">
210 <validator type="no_options" message="No cached LIANA resources available. Install them via Admin → Data Managers → Download LIANA Resources."/>
211 </options>
212 </param>
213 </when>
214 <when value="builtin">
215 <expand macro="param_resource_name"/>
216 </when>
217 </conditional>
218 </when>
219 <when value="resource">
220 <param argument="resource" type="data" format="tabular" label="Custom resource file (TSV)" help="Tab-separated file with at least two columns named 'ligand' and 'receptor'. Each row represents one ligand-receptor interaction. This resource will override the built-in database selection."/>
221 </when>
222 <when value="interactions">
223 <param argument="interactions" type="text" area="true" label="Ligand-receptor pairs (one per line)" help="Enter specific interactions to analyze in format: ligand,receptor (one pair per line, e.g., 'TGFB1,TGFBR1' or 'IL1A,IL1R1'). Use the same gene symbols as in your expression matrix. This list will override any built-in or custom resource file.">
224 <expand macro="sanitize_query"/>
225 </param>
226 </when>
227 </conditional>
228 </xml>
229 <!-- Multi-sample parameter macros -->
230 <xml name="param_sample_key">
231 <param argument="sample_key" type="text" value="@VALUE@" label="Sample key" help="Key in adata.obs for grouping by sample or condition context. Default: 'sample'.">
232 <expand macro="sanitize_query"/>
233 </param>
234 </xml>
235 <xml name="param_score_key">
236 <param argument="score_key" type="text" value="" optional="true" label="Score key" help="Column name of the score in liana_res. If empty, inferred from method.">
237 <expand macro="sanitize_query"/>
238 </param>
239 </xml>
240 <xml name="param_source_key">
241 <param argument="source_key" type="text" value="source" label="Source key" help="Column name of sender/source cell types in LIANA results. Default: 'source'.">
242 <expand macro="sanitize_query"/>
243 </param>
244 </xml>
245 <xml name="param_target_key">
246 <param argument="target_key" type="text" value="target" label="Target key" help="Column name of receiver/target cell types in LIANA results. Default: 'target'.">
247 <expand macro="sanitize_query"/>
248 </param>
249 </xml>
250 <xml name="param_ligand_key">
251 <param argument="ligand_key" type="text" value="ligand_complex" label="Ligand key" help="Column name of ligand in LIANA results. Default: 'ligand_complex'.">
252 <expand macro="sanitize_query"/>
253 </param>
254 </xml>
255 <xml name="param_receptor_key">
256 <param argument="receptor_key" type="text" value="receptor_complex" label="Receptor key" help="Column name of receptor in LIANA results. Default: 'receptor_complex'.">
257 <expand macro="sanitize_query"/>
258 </param>
259 </xml>
260 <xml name="params_multi_keys">
261 <expand macro="param_score_key"/>
262 <expand macro="param_uns_key"/>
263 <expand macro="param_source_key"/>
264 <expand macro="param_target_key"/>
265 <expand macro="param_ligand_key"/>
266 <expand macro="param_receptor_key"/>
267 </xml>
268
269 <!-- Plotting-specific parameter macros -->
270 <xml name="param_uns_key">
271 <param argument="uns_key" type="text" value="liana_res" label="Results key in adata.uns" help="Must match key_added from inference method">
272 <expand macro="sanitize_query"/>
273 </param>
274 </xml>
275 <xml name="param_plot_colour">
276 <param argument="colour" type="text" value="" optional="true" label="Color by column" help="Column name in liana_res DataFrame to map to dot color. E.g., 'magnitude_rank', 'specificity_rank', 'lr_means', or pvalue columns.">
277 <expand macro="sanitize_query"/>
278 </param>
279 </xml>
280 <xml name="param_plot_size">
281 <param argument="size" type="text" value="" optional="true" label="Size by column" help="Column name in liana_res DataFrame to map to dot size. Larger values = larger dots.">
282 <expand macro="sanitize_query"/>
283 </param>
284 </xml>
285 <xml name="param_misty_key">
286 <param argument="key" type="text" value="" optional="true" label="Function to use to sort the dataframe" help="">
287 <expand macro="sanitize_query"/>
288 </param>
289 </xml>
290 <xml name="param_source_labels">
291 <param argument="source_labels" type="text" value="" optional="true" label="Source (sender) cell types" help="Comma-separated list of source cell type labels. Empty = show all. Useful for focusing on specific signaling populations.">
292 <expand macro="sanitize_query"/>
293 </param>
294 </xml>
295 <xml name="param_target_labels">
296 <param argument="target_labels" type="text" value="" optional="true" label="Target (receiver) cell types" help="Comma-separated list of target cell type labels. Empty = show all. Useful for focusing on specific receiving populations.">
297 <expand macro="sanitize_query"/>
298 </param>
299 </xml>
300 <xml name="param_ligand_complex">
301 <param argument="ligand_complex" type="text" value="" optional="true" label="Ligand genes" help="Comma-separated ligand gene symbols to include. Empty = all genes. Example: IL6,TNF,TGFB1.">
302 <expand macro="sanitize_query"/>
303 </param>
304 </xml>
305 <xml name="param_receptor_complex">
306 <param argument="receptor_complex" type="text" value="" optional="true" label="Receptor genes" help="Comma-separated receptor gene symbols to include. Empty = all genes. Example: EGFR,FGFR1,PDGFRA.">
307 <expand macro="sanitize_query"/>
308 </param>
309 </xml>
310 <xml name="param_top_n">
311 <param argument="top_n" type="integer" value="" optional="true" min="1" label="Top N interactions" help="Number of top-ranked interactions to display."/>
312 </xml>
313 <xml name="param_orderby">
314 <param argument="orderby" type="text" value="" optional="true" label="Sort column" help="Column in LIANA results to sort by (used with top_n).">
315 <expand macro="sanitize_query"/>
316 </param>
317 </xml>
318 <xml name="param_orderby_ascending">
319 <param argument="orderby_ascending" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sort ascending" help="Sort by increasing (smallest to largest) values."/>
320 </xml>
321 <xml name="param_orderby_absolute">
322 <param argument="orderby_absolute" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sort by absolute value" help="Sort by absolute value magnitude (ignoring sign)."/>
323 </xml>
324 <xml name="param_inverse_colour">
325 <param argument="inverse_colour" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Apply -log10 transformation to color" help="If enabled: apply -log10 to color column (e.g., converts p-values to -log10(p)). Useful for p-value visualization."/>
326 </xml>
327 <xml name="param_inverse_size">
328 <param argument="inverse_size" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Apply -log10 transformation to size" help="If enabled: apply -log10 to size column (useful for p-values where smaller p = larger dots)."/>
329 </xml>
330 <xml name="param_cmap">
331 <param argument="cmap" type="select" label="Color scheme (matplotlib colormap)" help="Colormap for color column visualization. viridis/plasma: perceptually uniform; RdBu: diverging; sequential: Reds, Blues, etc. Default: viridis.">
332 <option value="viridis" selected="true">viridis - Perceptually uniform</option>
333 <option value="plasma">plasma</option>
334 <option value="inferno">inferno</option>
335 <option value="magma">magma</option>
336 <option value="cividis">cividis</option>
337 <option value="Greys">Greys</option>
338 <option value="Blues">Blues</option>
339 <option value="Greens">Greens</option>
340 <option value="Oranges">Oranges</option>
341 <option value="Reds">Reds</option>
342 <option value="YlOrBr">YlOrBr</option>
343 <option value="YlOrRd">YlOrRd</option>
344 <option value="OrRd">OrRd</option>
345 <option value="PuRd">PuRd</option>
346 <option value="RdPu">RdPu</option>
347 <option value="BuPu">BuPu</option>
348 <option value="GnBu">GnBu</option>
349 <option value="PuBu">PuBu</option>
350 <option value="YlGnBu">YlGnBu</option>
351 <option value="PuBuGn">PuBuGn</option>
352 <option value="BuGn">BuGn</option>
353 <option value="YlGn">YlGn</option>
354 <option value="PiYG">PiYG</option>
355 <option value="PRGn">PRGn</option>
356 <option value="BrBG">BrBG</option>
357 <option value="PuOr">PuOr</option>
358 <option value="RdGy">RdGy</option>
359 <option value="RdBu">RdBu</option>
360 <option value="RdBu_r">RdBu_r</option>
361 <option value="RdYlBu">RdYlBu</option>
362 <option value="RdYlGn">RdYlGn</option>
363 <option value="Spectral">Spectral</option>
364 <option value="coolwarm">coolwarm</option>
365 <option value="bwr">bwr</option>
366 <option value="seismic">seismic</option>
367 </param>
368 </xml>
369 <xml name="param_size_range">
370 <param name="size_range_min" type="integer" value="2" min="1" label="Minimum dot size (pixels)" help="Smallest dot size for minimum values. Default: 2 pixels."/>
371 <param name="size_range_max" type="integer" value="9" min="1" label="Maximum dot size (pixels)" help="Largest dot size for maximum values. Default: 9 pixels. Adjust range to make size differences more/less prominent."/>
372 </xml>
373 <xml name="param_figure_size" token_width="8" token_height="6">
374 <param name="figure_size_width" type="float" value="@WIDTH@" min="1" label="Figure width (inches)" help="Output plot width. Default: 8 inches."/>
375 <param name="figure_size_height" type="float" value="@HEIGHT@" min="1" label="Figure height (inches)" help="Output plot height. Default: 6 inches."/>
376 </xml>
377
378 <!-- Plotting command tokens -->
379 <token name="@CMD_PLOT_SOURCE_TARGET_LABELS@"><![CDATA[
380 #if str($method.source_labels) != '':
381 source_labels=[x.strip() for x in '$method.source_labels'.split(',')],
382 #end if
383 #if str($method.target_labels) != '':
384 target_labels=[x.strip() for x in '$method.target_labels'.split(',')],
385 #end if
386 ]]>
387 </token>
388 <token name="@CMD_PLOT_LIGAND_RECEPTOR_COMPLEX@"><![CDATA[
389 #if str($method.ligand_complex) != '':
390 ligand_complex=[x.strip() for x in '$method.ligand_complex'.split(',')],
391 #end if
392 #if str($method.receptor_complex) != '':
393 receptor_complex=[x.strip() for x in '$method.receptor_complex'.split(',')],
394 #end if
395 ]]>
396 </token>
397 <token name="@CMD_PLOT_TOP_N_ORDERBY@"><![CDATA[
398 #if str($method.top_n) != '':
399 top_n=$method.top_n,
400 #end if
401 #if str($method.orderby) != '':
402 orderby='$method.orderby',
403 #end if
404 orderby_ascending=$method.orderby_ascending,
405 orderby_absolute=$method.orderby_absolute,
406 ]]>
407 </token>
408
409 <!-- command macros -->
410 <xml name="version_command">
411 <version_command><![CDATA[python -c "import liana as li;print('liana version: %s' % li.__version__)"]]></version_command>
412 </xml>
413 <token name="@CMD_PRETTIFY_STDOUT@"><![CDATA[
414 | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed "s|'||g" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'
415 ]]>
416 </token>
417 <token name="@CMD_READ_INPUTS@"><![CDATA[
418 adata = sc.read_h5ad('anndata.h5ad')
419 ]]>
420 </token>
421 <!-- Resource param block for L-R methods: interactions | resource (file) | resource (cached from DM) | resource_name (API) -->
422 <token name="@CMD_RESOURCE_FOR_METHODS@"><![CDATA[
423 #if str($method.resource_selection.resource_type) == 'interactions':
424 interactions=[tuple(x.strip().split(',')) for x in '''$method.resource_selection.interactions'''.strip().split('\n') if x.strip()],
425 #else if str($method.resource_selection.resource_type) == 'resource':
426 resource=pd.read_csv('$method.resource_selection.resource', sep='\t'),
427 #else:
428 #if str($method.resource_selection.resource_api_cached.resource_source_selector) == 'cached':
429 resource=pd.read_csv(os.path.join('$method.resource_selection.resource_api_cached.resource_cached.fields.path', '$method.resource_selection.resource_api_cached.resource_cached.fields.value' + '.tsv'), sep='\t'),
430 #else:
431 resource_name='$method.resource_selection.resource_api_cached.resource_name',
432 #end if
433 #end if
434 ]]>
435 </token>
436 <!-- ln -s doesn't work here because the output is overwritten to the same file -->
437 <token name="@CMD@"><![CDATA[
438 cp '$adata' 'anndata.h5ad' &&
439 cat '$script_file' > '$hidden_output' &&
440 python '$script_file' >> '$hidden_output' &&
441 ls . >> '$hidden_output' &&
442 touch 'anndata_info.txt' &&
443 cat 'anndata_info.txt' @CMD_PRETTIFY_STDOUT@
444 ]]>
445 </token>
446 <token name="@CMD_IMPORTS@"><![CDATA[
447 import liana as li
448 import scanpy as sc
449 import pandas as pd
450 import os
451
452 ]]>
453 </token>
454 <token name="@CMD_ANNDATA_WRITE_OUTPUTS@"><![CDATA[
455 adata.write_h5ad('anndata.h5ad', compression='gzip')
456 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
457 print(adata, file=ainfo)
458 ]]>
459 </token>
460 </macros>