Mercurial > repos > iuc > snapatac2_preprocessing

comparison macros.xml @ 1:cec3e76eaf05 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
author iuc
date Thu, 23 May 2024 15:20:02 +0000
parents 00a6721e1f81
children 48d9421bf176
comparison
equal deleted inserted replaced
0:00a6721e1f81 1:cec3e76eaf05
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.5.3</token> 2 <token name="@TOOL_VERSION@">2.5.3</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@PROFILE@">23.0</token> 4 <token name="@PROFILE@">23.0</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>
7 <requirement type="package" version="5.18.0">plotly</requirement> 7 <requirement type="package" version="5.18.0">plotly</requirement>
8 <requirement type="package" version="0.2.1">python-kaleido</requirement> 8 <requirement type="package" version="0.2.1">python-kaleido</requirement>
10 <requirement type="package" version="14.0.1">pyarrow</requirement> 10 <requirement type="package" version="14.0.1">pyarrow</requirement>
11 <requirement type="package" version="0.11.3">python-igraph</requirement> 11 <requirement type="package" version="0.11.3">python-igraph</requirement>
12 <requirement type="package" version="0.8.33">hdbscan</requirement> 12 <requirement type="package" version="0.8.33">hdbscan</requirement>
13 <requirement type="package" version="0.0.9">harmonypy</requirement> 13 <requirement type="package" version="0.0.9">harmonypy</requirement>
14 <requirement type="package" version="1.7.4">scanorama</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>
15 <yield /> 18 <yield />
16 </xml> 19 </xml>
17 20
18 <token name="@PREP_ADATA@"><![CDATA[ 21 <token name="@PREP_ADATA@"><![CDATA[
19 cp '$method.adata' 'anndata.h5ad' && 22 cp '$method.adata' 'anndata.h5ad' &&
21 </token> 24 </token>
22 25
23 <token name="@CMD@"><![CDATA[ 26 <token name="@CMD@"><![CDATA[
24 cat '$script_file' > '$hidden_output' && 27 cat '$script_file' > '$hidden_output' &&
25 python '$script_file' >> '$hidden_output' && 28 python '$script_file' >> '$hidden_output' &&
26 touch 'anndata_info.txt' && 29 touch 'anndata_info.txt' &&
27 cat 'anndata_info.txt' @CMD_prettify_stdout@ 30 cat 'anndata_info.txt' @CMD_prettify_stdout@
28 ]]> 31 ]]>
29 </token> 32 </token>
30 33
31 <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' 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'
32 ]]></token> 35 ]]></token>
54 ]]> 57 ]]>
55 </token> 58 </token>
56 59
57 <xml name="dimentions_plot"> 60 <xml name="dimentions_plot">
58 <param argument="width" type="integer" value="500" label="Width of the plot"/> 61 <param argument="width" type="integer" value="500" label="Width of the plot"/>
59 <param argument="height" type="integer" value="400" label="Height of the plot"/> 62 <param argument="height" type="integer" value="400" label="Height of the plot"/>
60 </xml> 63 </xml>
61 64
62 <xml name="param_groupby"> 65 <xml name="param_groupby">
63 <param argument="groupby" type="text" label="The key of the observation grouping to consider"> 66 <param argument="groupby" type="text" label="The key of the observation grouping to consider">
64 <expand macro="sanitize_query" /> 67 <expand macro="sanitize_query" />
65 </param> 68 </param>
66 </xml> 69 </xml>
67 70
68 <xml name="out_file"> 71 <xml name="out_file">
69 <param name="out_file" type="select" optional="true" label="Type of output file"> 72 <param name="out_file" type="select" optional="true" label="Type of output plot">
70 <option value="png" selected="true">PNG</option> 73 <option value="png" selected="true">PNG</option>
71 <option value="svg">SVG</option> 74 <option value="svg">SVG</option>
72 <option value="pdf">PDF</option> 75 <option value="pdf">PDF</option>
73 </param> 76 </param>
74 </xml> 77 </xml>
75 <token name="@CMD_anndata_write_outputs@"><![CDATA[ 78 <token name="@CMD_anndata_write_outputs@"><![CDATA[
76 adata.write('anndata.h5ad') 79 adata.write('anndata.h5ad')
77 with open('anndata_info.txt','w', encoding='utf-8') as ainfo: 80 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
78 print(adata, file=ainfo) 81 print(adata, file=ainfo)
87 <param argument="width" type="integer" value="600" label="Width of the plot"/> 90 <param argument="width" type="integer" value="600" label="Width of the plot"/>
88 <param argument="height" type="integer" value="400" label="Height of the plot"/> 91 <param argument="height" type="integer" value="400" label="Height of the plot"/>
89 <expand macro="out_file"/> 92 <expand macro="out_file"/>
90 </xml> 93 </xml>
91 <xml name="param_shift"> 94 <xml name="param_shift">
92 <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"/> 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"/>
93 <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"/> 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"/>
94 </xml> 97 </xml>
95 <xml name="param_chunk_size" tokens="size"> 98 <xml name="param_chunk_size" tokens="size">
96 <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/> 99 <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/>
97 </xml> 100 </xml>
98 <xml name="min_max_frag_size"> 101 <xml name="min_max_frag_size">
99 <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/> 102 <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/>
100 <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/> 103 <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/>
101 </xml> 104 </xml>
102 <xml name="params_data_integration"> 105 <xml name="params_data_integration">
103 <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/> 106 <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/>
104 <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation"> 107 <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation">
105 <expand macro="sanitize_query"/> 108 <expand macro="sanitize_query"/>
106 </param> 109 </param>
107 <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider"> 110 <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider">
108 <expand macro="sanitize_query" /> 111 <expand macro="sanitize_query" />
109 </param> 112 </param>
110 <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/> 113 <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/>
111 </xml> 114 </xml>
112 <xml name="param_n_comps"> 115 <xml name="param_n_comps">
113 s <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."/> 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."/>
114 </xml> 117 </xml>
115 <xml name="param_random_state"> 118 <xml name="param_random_state">
116 <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/> 119 <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/>
117 </xml> 120 </xml>
118 <xml name="param_key_added" tokens="key_added"> 121 <xml name="param_key_added" tokens="key_added">
124 <xml name="genome_fasta"> 127 <xml name="genome_fasta">
125 <param argument="genome_fasta" type="text" label="A fasta file containing the genome sequences or a Genome object"/> 128 <param argument="genome_fasta" type="text" label="A fasta file containing the genome sequences or a Genome object"/>
126 </xml> 129 </xml>
127 <xml name="background"> 130 <xml name="background">
128 <param argument="background" type="text" optional="true" value="" label="A list of regions to be used as the background"> 131 <param argument="background" type="text" optional="true" value="" label="A list of regions to be used as the background">
129 <expand macro="sanitize_query"/> 132 <expand macro="sanitize_query"/>
130 </param> 133 </param>
131 </xml> 134 </xml>
132 <xml name="mat"> 135 <xml name="mat">
133 <param argument="peak_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by peak count matrix"/> 136 <param argument="peak_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by peak count matrix"/>
134 <param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene 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"/>
135 </xml> 138 </xml>
136 <xml name="param_network"> 139 <xml name="param_network">
137 <param argument="network" type="text" label="network"/> 140 <param argument="network" type="text" label="network"/>
138 </xml> 141 </xml>
139 <xml name="param_n_iterations"> 142 <xml name="param_n_iterations">
145 <citations> 148 <citations>
146 <citation type="doi">10.1038/s41592-023-02139-9</citation> 149 <citation type="doi">10.1038/s41592-023-02139-9</citation>
147 </citations> 150 </citations>
148 </xml> 151 </xml>
149 <xml name="render_plot_test"> 152 <xml name="render_plot_test">
150 <param name="width" value="650"/> 153 <param name="width" value="650"/>
151 <param name="height" value="450"/> 154 <param name="height" value="450"/>
152 </xml> 155 </xml>
153 <xml name="render_plot_matching_text"> 156 <xml name="render_plot_matching_text">
154 <has_text_matching expression="width = 650"/> 157 <has_text_matching expression="width = 650"/>
155 <has_text_matching expression="height = 450"/> 158 <has_text_matching expression="height = 450"/>
156 </xml> 159 </xml>
157 <xml name="param_counting_strategy"> 160 <xml name="param_counting_strategy">
158 <param argument="counting_strategy" type="select" label="he strategy to compute feature counts"> 161 <param argument="counting_strategy" type="select" label="he strategy to compute feature counts">
159 <option value="fragment">fragment</option> 162 <option value="fragment">fragment</option>