Mercurial > repos > iuc > snapatac2_clustering
annotate macros.xml @ 4:afb90d3485df draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 04112de6f91d4f848fe35d857c84c4b8a9fc980f
author | iuc |
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date | Tue, 23 Jul 2024 16:24:56 +0000 |
parents | 509baa4a2da0 |
children | d3ea0ba3d066 |
rev | line source |
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0
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
1 <macros> |
3
509baa4a2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents:
2
diff
changeset
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2 <token name="@TOOL_VERSION@">2.6.4</token> |
4
afb90d3485df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 04112de6f91d4f848fe35d857c84c4b8a9fc980f
iuc
parents:
3
diff
changeset
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3 <token name="@VERSION_SUFFIX@">1</token> |
0
af821711b356
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> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
5 <xml name="requirements"> |
af821711b356
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> |
3
509baa4a2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents:
2
diff
changeset
|
7 <requirement type="package" version="5.22.0">plotly</requirement> |
0
af821711b356
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> |
3
509baa4a2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents:
2
diff
changeset
|
9 <requirement type="package" version="1.1.0">polars</requirement> |
509baa4a2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents:
2
diff
changeset
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10 <requirement type="package" version="16.1.0">pyarrow</requirement> |
509baa4a2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents:
2
diff
changeset
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11 <requirement type="package" version="0.11.6">python-igraph</requirement> |
509baa4a2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents:
2
diff
changeset
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12 <requirement type="package" version="0.8.37">hdbscan</requirement> |
509baa4a2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents:
2
diff
changeset
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13 <requirement type="package" version="0.0.10">harmonypy</requirement> |
0
af821711b356
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
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
0
diff
changeset
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15 <requirement type="package" version="3.0.1">macs3</requirement> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
0
diff
changeset
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16 <requirement type="package" version="0.70.16">multiprocess</requirement> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
0
diff
changeset
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17 <requirement type="package" version="0.10.2">leidenalg</requirement> |
0
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
18 <yield /> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
19 </xml> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
20 |
af821711b356
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[ |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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22 cp '$method.adata' 'anndata.h5ad' && |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
23 ]]> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
24 </token> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
25 |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
26 <token name="@CMD@"><![CDATA[ |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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27 cat '$script_file' > '$hidden_output' && |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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28 python '$script_file' >> '$hidden_output' && |
1
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
0
diff
changeset
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29 touch 'anndata_info.txt' && |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
0
diff
changeset
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30 cat 'anndata_info.txt' @CMD_prettify_stdout@ |
0
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
31 ]]> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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32 </token> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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33 |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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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' |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
35 ]]></token> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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36 |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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37 <token name="@CMD_imports@"><![CDATA[ |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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38 import snapatac2 as sa |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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39 import os |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
40 ]]> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
41 </token> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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42 <xml name="sanitize_query" token_validinitial="string.printable"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
43 <sanitizer> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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44 <valid initial="@VALIDINITIAL@"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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45 <remove value="'" /> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
46 </valid> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
47 </sanitizer> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
48 </xml> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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49 |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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50 <xml name="inputs_anndata"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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51 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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52 </xml> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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53 |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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54 <token name="@CMD_read_inputs@"><![CDATA[ |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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55 |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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56 adata = sa.read('anndata.h5ad', backed = None) |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
|
57 ]]> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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58 </token> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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59 |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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60 <xml name="dimentions_plot"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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61 <param argument="width" type="integer" value="500" label="Width of the plot"/> |
1
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
0
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62 <param argument="height" type="integer" value="400" label="Height of the plot"/> |
0
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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63 </xml> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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64 |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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65 <xml name="param_groupby"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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66 <param argument="groupby" type="text" label="The key of the observation grouping to consider"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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67 <expand macro="sanitize_query" /> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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68 </param> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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69 </xml> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
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70 |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
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71 <xml name="out_file"> |
1
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
0
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72 <param name="out_file" type="select" optional="true" label="Type of output plot"> |
0
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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73 <option value="png" selected="true">PNG</option> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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74 <option value="svg">SVG</option> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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75 <option value="pdf">PDF</option> |
1
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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76 </param> |
0
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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77 </xml> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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78 <token name="@CMD_anndata_write_outputs@"><![CDATA[ |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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79 adata.write('anndata.h5ad') |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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80 with open('anndata_info.txt','w', encoding='utf-8') as ainfo: |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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81 print(adata, file=ainfo) |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
changeset
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82 ]]> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff
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83 </token> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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84 <xml name="inputs_common_advanced"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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85 <section name="advanced_common" title="Advanced Options" expanded="false"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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86 <param name="show_log" type="boolean" checked="false" label="Output Log?" /> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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87 </section> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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88 </xml> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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89 <xml name="params_render_plot"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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90 <param argument="width" type="integer" value="600" label="Width of the plot"/> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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91 <param argument="height" type="integer" value="400" label="Height of the plot"/> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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92 <expand macro="out_file"/> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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93 </xml> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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94 <xml name="param_shift"> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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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"/> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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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
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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97 </xml> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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98 <xml name="param_chunk_size" tokens="size"> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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99 <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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100 </xml> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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101 <xml name="min_max_frag_size"> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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102 <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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103 <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/> |
0
af821711b356
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104 </xml> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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105 <xml name="params_data_integration"> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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106 <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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107 <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation"> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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108 <expand macro="sanitize_query"/> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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109 </param> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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110 <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider"> |
0
af821711b356
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111 <expand macro="sanitize_query" /> |
af821711b356
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112 </param> |
1
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113 <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/> |
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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114 </xml> |
0
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115 <xml name="param_n_comps"> |
1
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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
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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117 </xml> |
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118 <xml name="param_random_state"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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119 <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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120 </xml> |
af821711b356
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121 <xml name="param_key_added" tokens="key_added"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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122 <param argument="key_added" type="text" value="@KEY_ADDED@" label="`adata.obs` key under which t add cluster labels"/> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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123 </xml> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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124 <xml name="param_use_rep"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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125 <param argument="use_rep" type="text" value="X_spectral" label="Use the indicated representation in `.obsm`"/> |
af821711b356
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126 </xml> |
af821711b356
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127 <xml name="genome_fasta"> |
af821711b356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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128 <param argument="genome_fasta" type="text" label="A fasta file containing the genome sequences or a Genome object"/> |
af821711b356
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129 </xml> |
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130 <xml name="background"> |
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131 <param argument="background" type="text" optional="true" value="" label="A list of regions to be used as the background"> |
1
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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132 <expand macro="sanitize_query"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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133 </param> |
0
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134 </xml> |
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135 <xml name="mat"> |
af821711b356
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136 <param argument="peak_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by peak count matrix"/> |
1
8f8bef61fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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137 <param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/> |
0
af821711b356
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138 </xml> |
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139 <xml name="param_network"> |
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140 <param argument="network" type="text" label="network"/> |
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141 </xml> |
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142 <xml name="param_n_iterations"> |
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143 <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform" |
af821711b356
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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."/> |
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145 </xml> |
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146 |
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147 <xml name="citations"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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148 <citations> |
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149 <citation type="doi">10.1038/s41592-023-02139-9</citation> |
af821711b356
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150 </citations> |
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151 </xml> |
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152 <xml name="render_plot_test"> |
1
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153 <param name="width" value="650"/> |
0
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154 <param name="height" value="450"/> |
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155 </xml> |
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156 <xml name="render_plot_matching_text"> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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157 <has_text_matching expression="width = 650"/> |
0
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158 <has_text_matching expression="height = 450"/> |
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159 </xml> |
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160 <xml name="param_counting_strategy"> |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
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161 <param argument="counting_strategy" type="select" label="The strategy to compute feature counts"> |
509baa4a2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
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162 <option value="fragment">"fragment": based on the number of fragments that overlap with a region of interest</option> |
509baa4a2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
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163 <option value="insertion" selected="true">"insertion": based on the number of insertions that overlap with a region of interest</option> |
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164 <option value="paired-insertion">"paired-insertion": similar to "insertion", but it only counts the insertions once if the pair of insertions of a fragment are both within the same region of interest</option> |
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165 </param> |
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166 </xml> |
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167 |
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168 <token name="@CMD_params_data_integration@"><![CDATA[ |
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169 use_rep = '$method.use_rep', |
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170 #if $method.use_dims != '' |
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171 #set $dims = ([x.strip() for x in str($method.use_dims).split(',')]) |
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172 use_dims=$dims, |
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173 #end if |
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174 #if $method.groupby != '' |
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175 #set $groupby = ([x.strip() for x in str($method.groupby).split(',')]) |
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176 groupby=$groupby, |
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177 #end if |
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178 #if $method.key_added != '' |
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179 key_added = '$method.key_added', |
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180 #end if |
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181 ]]> |
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182 </token> |
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183 |
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184 <token name="@CMD_params_render_plot@"><![CDATA[ |
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185 width = $method.width, |
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186 height = $method.height, |
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187 out_file = 'plot.$method.out_file', |
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188 ]]> |
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189 </token> |
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190 </macros> |