annotate macros.xml @ 2:48d9421bf176 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
author iuc
date Fri, 05 Jul 2024 11:06:01 +0000
parents cec3e76eaf05
children 4ecdea4cbea1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1 <macros>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
2 <token name="@TOOL_VERSION@">2.5.3</token>
2
48d9421bf176 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents: 1
diff changeset
3 <token name="@VERSION_SUFFIX@">2</token>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
4 <token name="@PROFILE@">23.0</token>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
5 <xml name="requirements">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
7 <requirement type="package" version="5.18.0">plotly</requirement>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
8 <requirement type="package" version="0.2.1">python-kaleido</requirement>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
9 <requirement type="package" version="0.19.19">polars</requirement>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
10 <requirement type="package" version="14.0.1">pyarrow</requirement>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
11 <requirement type="package" version="0.11.3">python-igraph</requirement>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
12 <requirement type="package" version="0.8.33">hdbscan</requirement>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
13 <requirement type="package" version="0.0.9">harmonypy</requirement>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
14 <requirement type="package" version="1.7.4">scanorama</requirement>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
15 <requirement type="package" version="3.0.1">macs3</requirement>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
16 <requirement type="package" version="0.70.16">multiprocess</requirement>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
17 <requirement type="package" version="0.10.2">leidenalg</requirement>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
18 <yield />
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
19 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
20
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
21 <token name="@PREP_ADATA@"><![CDATA[
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
22 cp '$method.adata' 'anndata.h5ad' &&
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
23 ]]>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
24 </token>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
25
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
26 <token name="@CMD@"><![CDATA[
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
27 cat '$script_file' > '$hidden_output' &&
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
28 python '$script_file' >> '$hidden_output' &&
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
29 touch 'anndata_info.txt' &&
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
30 cat 'anndata_info.txt' @CMD_prettify_stdout@
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
31 ]]>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
32 </token>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
33
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
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'
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
35 ]]></token>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
36
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
37 <token name="@CMD_imports@"><![CDATA[
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
38 import snapatac2 as sa
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
39 import os
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
40 ]]>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
41 </token>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
42 <xml name="sanitize_query" token_validinitial="string.printable">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
43 <sanitizer>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
44 <valid initial="@VALIDINITIAL@">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
45 <remove value="&apos;" />
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
46 </valid>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
47 </sanitizer>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
48 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
49
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
50 <xml name="inputs_anndata">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
51 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
52 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
53
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
54 <token name="@CMD_read_inputs@"><![CDATA[
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
55
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
56 adata = sa.read('anndata.h5ad', backed = None)
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
57 ]]>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
58 </token>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
59
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
60 <xml name="dimentions_plot">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
61 <param argument="width" type="integer" value="500" label="Width of the plot"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
62 <param argument="height" type="integer" value="400" label="Height of the plot"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
63 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
64
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
65 <xml name="param_groupby">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
66 <param argument="groupby" type="text" label="The key of the observation grouping to consider">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
67 <expand macro="sanitize_query" />
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
68 </param>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
69 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
70
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
71 <xml name="out_file">
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
72 <param name="out_file" type="select" optional="true" label="Type of output plot">
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
73 <option value="png" selected="true">PNG</option>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
74 <option value="svg">SVG</option>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
75 <option value="pdf">PDF</option>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
76 </param>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
77 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
78 <token name="@CMD_anndata_write_outputs@"><![CDATA[
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
79 adata.write('anndata.h5ad')
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
80 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
81 print(adata, file=ainfo)
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
82 ]]>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
83 </token>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
84 <xml name="inputs_common_advanced">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
85 <section name="advanced_common" title="Advanced Options" expanded="false">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
86 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
87 </section>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
88 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
89 <xml name="params_render_plot">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
90 <param argument="width" type="integer" value="600" label="Width of the plot"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
91 <param argument="height" type="integer" value="400" label="Height of the plot"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
92 <expand macro="out_file"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
93 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
94 <xml name="param_shift">
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
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"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
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"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
97 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
98 <xml name="param_chunk_size" tokens="size">
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
99 <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
100 </xml>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
101 <xml name="min_max_frag_size">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
102 <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
103 <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
104 </xml>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
105 <xml name="params_data_integration">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
106 <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
107 <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
108 <expand macro="sanitize_query"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
109 </param>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
110 <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider">
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
111 <expand macro="sanitize_query" />
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
112 </param>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
113 <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
114 </xml>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
115 <xml name="param_n_comps">
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
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."/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
117 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
118 <xml name="param_random_state">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
119 <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
120 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
121 <xml name="param_key_added" tokens="key_added">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
122 <param argument="key_added" type="text" value="@KEY_ADDED@" label="`adata.obs` key under which t add cluster labels"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
123 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
124 <xml name="param_use_rep">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
125 <param argument="use_rep" type="text" value="X_spectral" label="Use the indicated representation in `.obsm`"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
126 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
127 <xml name="genome_fasta">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
128 <param argument="genome_fasta" type="text" label="A fasta file containing the genome sequences or a Genome object"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
129 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
130 <xml name="background">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
131 <param argument="background" type="text" optional="true" value="" label="A list of regions to be used as the background">
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
132 <expand macro="sanitize_query"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
133 </param>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
134 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
135 <xml name="mat">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
136 <param argument="peak_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by peak count matrix"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
137 <param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
138 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
139 <xml name="param_network">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
140 <param argument="network" type="text" label="network"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
141 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
142 <xml name="param_n_iterations">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
143 <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform"
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
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."/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
145 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
146
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
147 <xml name="citations">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
148 <citations>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
149 <citation type="doi">10.1038/s41592-023-02139-9</citation>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
150 </citations>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
151 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
152 <xml name="render_plot_test">
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
153 <param name="width" value="650"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
154 <param name="height" value="450"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
155 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
156 <xml name="render_plot_matching_text">
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
157 <has_text_matching expression="width = 650"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
158 <has_text_matching expression="height = 450"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
159 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
160 <xml name="param_counting_strategy">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
161 <param argument="counting_strategy" type="select" label="he strategy to compute feature counts">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
162 <option value="fragment">fragment</option>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
163 <option value="insertion" selected="true">insertion</option>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
164 <option value="paired-insertion">paired-insertion</option>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
165 </param>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
166 </xml>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
167
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
168 <token name="@CMD_params_data_integration@"><![CDATA[
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
169 use_rep = '$method.use_rep',
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
170 #if $method.use_dims != ''
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
171 #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
172 use_dims=$dims,
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
173 #end if
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
174 #if $method.groupby != ''
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
175 #set $groupby = ([x.strip() for x in str($method.groupby).split(',')])
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
176 groupby=$groupby,
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
177 #end if
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
178 #if $method.key_added != ''
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
179 key_added = '$method.key_added',
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
180 #end if
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
181 ]]>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
182 </token>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
183
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
184 <token name="@CMD_params_render_plot@"><![CDATA[
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
185 width = $method.width,
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
186 height = $method.height,
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
187 out_file = 'plot.$method.out_file',
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
188 ]]>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
189 </token>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
190 </macros>