Mercurial > repos > iuc > snapatac2_preprocessing

comparison macros.xml @ 0:b2844c6efb72 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
author iuc
date Fri, 05 Jul 2024 11:05:36 +0000
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children e3b85e48487b
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-1:000000000000 0:b2844c6efb72
1 <macros>
2 <token name="@TOOL_VERSION@">2.5.3</token>
3 <token name="@VERSION_SUFFIX@">2</token>
4 <token name="@PROFILE@">23.0</token>
5 <xml name="requirements">
6 <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>
7 <requirement type="package" version="5.18.0">plotly</requirement>
8 <requirement type="package" version="0.2.1">python-kaleido</requirement>
9 <requirement type="package" version="0.19.19">polars</requirement>
10 <requirement type="package" version="14.0.1">pyarrow</requirement>
11 <requirement type="package" version="0.11.3">python-igraph</requirement>
12 <requirement type="package" version="0.8.33">hdbscan</requirement>
13 <requirement type="package" version="0.0.9">harmonypy</requirement>
14 <requirement type="package" version="1.7.4">scanorama</requirement>
15 <requirement type="package" version="3.0.1">macs3</requirement>
16 <requirement type="package" version="0.70.16">multiprocess</requirement>
17 <requirement type="package" version="0.10.2">leidenalg</requirement>
18 <yield />
19 </xml>
20
21 <token name="@PREP_ADATA@"><![CDATA[
22 cp '$method.adata' 'anndata.h5ad' &&
23 ]]>
24 </token>
25
26 <token name="@CMD@"><![CDATA[
27 cat '$script_file' > '$hidden_output' &&
28 python '$script_file' >> '$hidden_output' &&
29 touch 'anndata_info.txt' &&
30 cat 'anndata_info.txt' @CMD_prettify_stdout@
31 ]]>
32 </token>
33
34 <token name="@CMD_prettify_stdout@"><![CDATA[ | 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'
35 ]]></token>
36
37 <token name="@CMD_imports@"><![CDATA[
38 import snapatac2 as sa
39 import os
40 ]]>
41 </token>
42 <xml name="sanitize_query" token_validinitial="string.printable">
43 <sanitizer>
44 <valid initial="@VALIDINITIAL@">
45 <remove value="&apos;" />
46 </valid>
47 </sanitizer>
48 </xml>
49
50 <xml name="inputs_anndata">
51 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
52 </xml>
53
54 <token name="@CMD_read_inputs@"><![CDATA[
55
56 adata = sa.read('anndata.h5ad', backed = None)
57 ]]>
58 </token>
59
60 <xml name="dimentions_plot">
61 <param argument="width" type="integer" value="500" label="Width of the plot"/>
62 <param argument="height" type="integer" value="400" label="Height of the plot"/>
63 </xml>
64
65 <xml name="param_groupby">
66 <param argument="groupby" type="text" label="The key of the observation grouping to consider">
67 <expand macro="sanitize_query" />
68 </param>
69 </xml>
70
71 <xml name="out_file">
72 <param name="out_file" type="select" optional="true" label="Type of output plot">
73 <option value="png" selected="true">PNG</option>
74 <option value="svg">SVG</option>
75 <option value="pdf">PDF</option>
76 </param>
77 </xml>
78 <token name="@CMD_anndata_write_outputs@"><![CDATA[
79 adata.write('anndata.h5ad')
80 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
81 print(adata, file=ainfo)
82 ]]>
83 </token>
84 <xml name="inputs_common_advanced">
85 <section name="advanced_common" title="Advanced Options" expanded="false">
86 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
87 </section>
88 </xml>
89 <xml name="params_render_plot">
90 <param argument="width" type="integer" value="600" label="Width of the plot"/>
91 <param argument="height" type="integer" value="400" label="Height of the plot"/>
92 <expand macro="out_file"/>
93 </xml>
94 <xml name="param_shift">
95 <param argument="shift_left" type="integer" value="4" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/>
96 <param argument="shift_right" type="integer" value="-5" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/>
97 </xml>
98 <xml name="param_chunk_size" tokens="size">
99 <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/>
100 </xml>
101 <xml name="min_max_frag_size">
102 <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/>
103 <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/>
104 </xml>
105 <xml name="params_data_integration">
106 <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/>
107 <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation">
108 <expand macro="sanitize_query"/>
109 </param>
110 <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider">
111 <expand macro="sanitize_query" />
112 </param>
113 <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/>
114 </xml>
115 <xml name="param_n_comps">
116 <param argument="n_comps" type="integer" value="30" label="Number of dimensions to keep" help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30."/>
117 </xml>
118 <xml name="param_random_state">
119 <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/>
120 </xml>
121 <xml name="param_key_added" tokens="key_added">
122 <param argument="key_added" type="text" value="@KEY_ADDED@" label="`adata.obs` key under which t add cluster labels"/>
123 </xml>
124 <xml name="param_use_rep">
125 <param argument="use_rep" type="text" value="X_spectral" label="Use the indicated representation in `.obsm`"/>
126 </xml>
127 <xml name="genome_fasta">
128 <param argument="genome_fasta" type="text" label="A fasta file containing the genome sequences or a Genome object"/>
129 </xml>
130 <xml name="background">
131 <param argument="background" type="text" optional="true" value="" label="A list of regions to be used as the background">
132 <expand macro="sanitize_query"/>
133 </param>
134 </xml>
135 <xml name="mat">
136 <param argument="peak_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by peak count matrix"/>
137 <param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/>
138 </xml>
139 <xml name="param_network">
140 <param argument="network" type="text" label="network"/>
141 </xml>
142 <xml name="param_n_iterations">
143 <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform"
144 help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/>
145 </xml>
146
147 <xml name="citations">
148 <citations>
149 <citation type="doi">10.1038/s41592-023-02139-9</citation>
150 </citations>
151 </xml>
152 <xml name="render_plot_test">
153 <param name="width" value="650"/>
154 <param name="height" value="450"/>
155 </xml>
156 <xml name="render_plot_matching_text">
157 <has_text_matching expression="width = 650"/>
158 <has_text_matching expression="height = 450"/>
159 </xml>
160 <xml name="param_counting_strategy">
161 <param argument="counting_strategy" type="select" label="he strategy to compute feature counts">
162 <option value="fragment">fragment</option>
163 <option value="insertion" selected="true">insertion</option>
164 <option value="paired-insertion">paired-insertion</option>
165 </param>
166 </xml>
167
168 <token name="@CMD_params_data_integration@"><![CDATA[
169 use_rep = '$method.use_rep',
170 #if $method.use_dims != ''
171 #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
172 use_dims=$dims,
173 #end if
174 #if $method.groupby != ''
175 #set $groupby = ([x.strip() for x in str($method.groupby).split(',')])
176 groupby=$groupby,
177 #end if
178 #if $method.key_added != ''
179 key_added = '$method.key_added',
180 #end if
181 ]]>
182 </token>
183
184 <token name="@CMD_params_render_plot@"><![CDATA[
185 width = $method.width,
186 height = $method.height,
187 out_file = 'plot.$method.out_file',
188 ]]>
189 </token>
190 </macros>