Mercurial > repos > iuc > snapatac2_plotting

annotate macros.xml @ 6:1ac4a5f05f33 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
author iuc
date Tue, 25 Nov 2025 16:41:12 +0000
parents 05bd4db20227
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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1 <macros>
6
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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2 <token name="@TOOL_VERSION@">2.8.0</token>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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3 <token name="@VERSION_SUFFIX@">0</token>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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4 <token name="@PROFILE@">24.0</token>
5
05bd4db20227 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit a9dc6c2d00d4488dfb751609bac74b19f241e06a
iuc
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5 <xml name="xrefs">
05bd4db20227 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit a9dc6c2d00d4488dfb751609bac74b19f241e06a
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6 <xrefs>
05bd4db20227 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit a9dc6c2d00d4488dfb751609bac74b19f241e06a
iuc
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7 <xref type="bio.tools">snapatac</xref>
05bd4db20227 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit a9dc6c2d00d4488dfb751609bac74b19f241e06a
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8 </xrefs>
05bd4db20227 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit a9dc6c2d00d4488dfb751609bac74b19f241e06a
iuc
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9 </xml>
0
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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10 <xml name="requirements">
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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11 <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>
6
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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12 <requirement type="package" version="0.8.37">hdbscan</requirement>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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13 <requirement type="package" version="0.10.2">leidenalg</requirement>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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14 <requirement type="package" version="0.5.7">umap-learn</requirement>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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15 <requirement type="package" version="3.0.4">xgboost</requirement>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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16 <requirement type="package" version="0.2.1">python-kaleido</requirement>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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17 <requirement type="package" version="1.31.0">polars</requirement>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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18 <requirement type="package" version="5.24.1">plotly</requirement>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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19 <requirement type="package" version="0.2.1">python-kaleido</requirement>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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20 <requirement type="package" version="0.0.10">harmonypy</requirement>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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21 <requirement type="package" version="1.7.4">scanorama</requirement>
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0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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22 <yield />
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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23 </xml>
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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24
6
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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25 <!-- command section -->
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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26 <token name="@CMD_PREP_ADATA@"><![CDATA[
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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27 ## ln -s does not work here
0
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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28 cp '$method.adata' 'anndata.h5ad' &&
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1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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29 ]]></token>
0
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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30 <token name="@CMD@"><![CDATA[
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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31 cat '$script_file' > '$hidden_output' &&
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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32 python '$script_file' >> '$hidden_output' &&
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fecf9664c885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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33 touch 'anndata_info.txt' &&
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1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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34 cat 'anndata_info.txt' @CMD_PRETTIFY_STDOUT@
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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35 ]]></token>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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36 <token name="@CMD_PRETTIFY_STDOUT@"><![CDATA[
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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37 | 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'
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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38 ]]></token>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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39 <token name="@CMD_GET_GFF@"><![CDATA[
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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40 #if $method.gff_file_condi.gffSource == 'cached':
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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41 ln -s '$method.gff_file_condi.gff_pre_installed.fields.path' gff &&
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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42 #else:
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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43 ln -s '$method.gff_file_condi.gff_history' gff &&
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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44 #end if
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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45 ]]></token>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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46 <token name="@CMD_GET_FASTA@"><![CDATA[
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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47 #if $method.fasta_file_condi.fastaSource == 'indexed':
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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48 zcat '$method.fasta_file_condi.fasta_pre_installed.fields.path' > fasta.fa &&
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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49 echo "Using built-in FASTA: '$method.fasta_file_condi.fasta_pre_installed.fields.name'" >&2 &&
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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50 #else:
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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51 #if $method.fasta_file_condi.fasta_history.ext.endswith('.gz')
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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52 zcat '$method.fasta_file_condi.fasta_history' > fasta.fa &&
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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53 #else:
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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54 ln -s '$method.fasta_file_condi.fasta_history' fasta.fa &&
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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55 #end if
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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56 #end if
0
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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57 ]]></token>
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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58
6
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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59 <!-- Config section -->
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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60 <token name="@CONF_IMPORTS@"><![CDATA[
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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61 import snapatac2 as snap
0
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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62 import os
6
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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63 ]]></token>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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64 <token name="@CONF_READ_INPUTS@"><![CDATA[
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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65 adata = snap.read('anndata.h5ad', backed = None)
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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66 ]]></token>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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67 <token name="@CONF_ANNDATA_WRITE_OUTPUTS@"><![CDATA[
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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68 adata.write_h5ad('anndata.h5ad.gz', compression='gzip')
0
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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69 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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70 print(adata, file=ainfo)
6
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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71 ]]></token>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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72 <token name="@CONF_PARAMS_RENDER_PLOT@"><![CDATA[
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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73 width = $method.width,
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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74 height = $method.height,
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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75 show = False,
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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76 interactive = False,
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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77 out_file = 'plot.$method.out_file',
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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78 ]]></token>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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79 <token name="@CONF_PARAMS_DATA_INTEGRATION@"><![CDATA[
0
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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80 use_rep = '$method.use_rep',
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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81 #if $method.use_dims != ''
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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82 #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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83 use_dims=$dims,
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84 #end if
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85 #if $method.groupby != ''
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86 #set $groupby = ([x.strip() for x in str($method.groupby).split(',')])
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87 groupby=$groupby,
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88 #end if
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89 #if $method.key_added != ''
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90 key_added = '$method.key_added',
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91 #end if
6
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92 ]]></token>
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93 <token name="@CONF_IMPORT_MEME@"><![CDATA[
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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94 motifs = read_motifs("input.meme")
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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95 for motif in motifs:
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96 motif.name = motif.id.split('+')[0]
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97
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98 unique_motifs = {}
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99 for motif in motifs:
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100 name = motif.name
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101 if (
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102 name not in unique_motifs or
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103 unique_motifs[name].info_content() < motif.info_content()
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104 ):
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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105 unique_motifs[name] = motif
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106 motifs = list(unique_motifs.values())
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107
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108
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109 #else:
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110 motifs = read_motifs("input.meme")
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111 for motif in motifs:
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112 motif.name = motif.id.split('_')[0]
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113 motif.family = motif.id.split('+')[-1]
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114 ]]></token>
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115
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116 <!-- input section -->
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117 <xml name="sanitize_query" token_validinitial="string.printable">
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118 <sanitizer>
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119 <valid initial="@VALIDINITIAL@">
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120 <remove value="&apos;" />
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121 <yield/>
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122 </valid>
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123 </sanitizer>
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124 </xml>
0
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125
6
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126 <xml name="param_inputs_anndata" token_multiple="false" token_label="Annotated data matrix">
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127 <param name="adata" type="data" multiple="@MULTIPLE@" format="h5ad" label="@LABEL@"/>
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128 </xml>
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129 <xml name="param_groupby">
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130 <param argument="groupby" type="text" label="The key of the observation grouping to consider">
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131 <expand macro="sanitize_query" />
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132 </param>
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133 </xml>
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134 <xml name="param_common_advanced">
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135 <section name="advanced_common" title="Advanced Options" expanded="false">
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136 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
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137 </section>
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138 </xml>
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139 <xml name="param_render_plot">
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140 <param argument="width" type="integer" value="600" label="Width of the plot"/>
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141 <param argument="height" type="integer" value="400" label="Height of the plot"/>
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142 <param name="out_file" type="select" optional="true" label="Type of output plot">
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143 <option value="png" selected="true">PNG</option>
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144 <option value="svg">SVG</option>
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145 <option value="pdf">PDF</option>
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146 <option value="html">HTML</option>
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147 </param>
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148 </xml>
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149 <xml name="param_shift" tokens="varname" token_value="0" token_label="Insertion site correction for the left end">
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150 <param argument="@VARNAME@" type="integer" value="@VALUE@" label="@LABEL@" help="Note this has no effect on single-end reads"/>
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151 </xml>
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152 <xml name="param_chunk_size" tokens="size">
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153 <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/>
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154 </xml>
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155 <xml name="param_min_max_frag_size">
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156 <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/>
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157 <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/>
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158 </xml>
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159 <xml name="param_data_integration">
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160 <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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161 <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation">
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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162 <expand macro="sanitize_query"/>
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163 </param>
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164 <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider">
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165 <expand macro="sanitize_query" />
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166 </param>
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167 <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/>
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168 </xml>
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169 <xml name="param_random_state" token_label="Seed of the random state generator" token_help="">
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170 <param argument="random_state" type="integer" value="0" label="@LABEL@" help="@HELP@"/>
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171 </xml>
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172 <xml name="param_key_added" tokens="key_added">
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173 <param argument="key_added" type="text" value="@KEY_ADDED@" label="`adata.obs` key under which t add cluster labels"/>
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174 </xml>
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175 <xml name="param_use_rep" token_label="Use the indicated representation in `.obsm`">
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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176 <param argument="use_rep" type="text" value="X_spectral" label="@LABEL@"/>
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177 </xml>
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178 <xml name="param_n_iterations">
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179 <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform"
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180 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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181 </xml>
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182 <xml name="param_counting_strategy">
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183 <param argument="counting_strategy" type="select" label="The strategy to compute feature counts">
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184 <option value="fragment">"fragment": based on the number of fragments that overlap with a region of interest</option>
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185 <option value="insertion">"insertion": based on the number of insertions that overlap with a region of interest</option>
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186 <option value="paired-insertion" selected="true">"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>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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187 </param>
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188 </xml>
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189 <xml name="param_chrom_sizes">
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190 <param argument="chrom_sizes" type="data" format="tabular" label="Chromosome sizes" help="First column the chromosome name and second column the size"/>
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191 </xml>
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192 <xml name="param_genome_fasta">
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193 <conditional name="fasta_file_condi">
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194 <param name="fastaSource" type="select" label="Select a built-in FASTA or one from your history" help="Choose history if you don't see the correct FASTA.">
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195 <option value="indexed" selected="true">Use a built-in FASTA</option>
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196 <option value="history">Use a FASTA from history</option>
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197 </param>
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198 <when value="indexed">
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199 <param name="fasta_pre_installed" type="select" label="Select a FASTA file" help="Select the FASTA file from a list of pre-installed genomes">
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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200 <options from_data_table="all_fasta">
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201 <filter type="sort_by" column="2" />
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202 </options>
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203 </param>
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204 </when>
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205 <when value="history">
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206 <param name="fasta_history" type="data" format="fasta,fasta.gz" label="FASTA file" />
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207 </when>
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208 </conditional>
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209 </xml>
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210 <xml name="param_gene_anno">
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211 <conditional name="gff_file_condi">
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212 <param name="gffSource" type="select" label="Select a built-in GFF file or one from your history" help="Choose history if you don't see the correct GFF" >
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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213 <option value="cached" selected="true">Use a built-in GFF</option>
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214 <option value="history">Use a GFF from history</option>
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215 </param>
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216 <when value="cached">
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217 <param name="gff_pre_installed" type="select" label="Select a GFF file" help="Select the GFF from a list of pre-installed files">
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218 <options from_data_table="gene_sets">
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219 <filter type="sort_by" column="1" />
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220 </options>
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221 </param>
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222 </when>
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223 <when value="history">
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224 <param name="gff_history" type="data" format="gff3.gz" label="Select a GFF file" help="Make sure that the GFF corresponds to the same genome as the FASTA"/>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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225 </when>
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226 </conditional>
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227 </xml>
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228 <xml name="param_n_comps" token_value="30" token_label="Number of dimensions to keep" token_help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30.">
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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229 <param argument="n_comps" type="integer" value="@VALUE@" label="@LABEL@" help="@HELP@"/>
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230 </xml>
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231 <xml name="param_meme_table">
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232 <param name="motifs" type="select" label="Select list of transcription factor motifs">
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233 <options from_data_table="meme">
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234 <filter type="sort_by" column="2" />
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235 </options>
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236 </param>
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237 </xml>
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238
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239
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240 <!-- test section -->
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241 <xml name="test_param_render_plot">
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242 <param name="width" value="650"/>
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243 <param name="height" value="450"/>
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244 </xml>
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245 <xml name="test_render_plot_matching_text">
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246 <has_text_matching expression="width = 650"/>
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247 <has_text_matching expression="height = 450"/>
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248 </xml>
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249
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250
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251 <xml name="citations">
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252 <citations>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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253 <citation type="doi">10.1038/s41592-023-02139-9</citation>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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254 </citations>
1ac4a5f05f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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255 </xml>
0
0cfd2d2f7351 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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256 </macros>