Mercurial > repos > iuc > episcanpy_preprocess

annotate preprocess.xml @ 0:307f05e02a03 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
author iuc
date Tue, 18 Apr 2023 13:17:48 +0000
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children ed9b88a259f1
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307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
1 <tool id="episcanpy_preprocess" name="scATAC-seq Preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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2 <description>with EpiScanpy</description>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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3 <macros>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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4 <import>macros.xml</import>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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5 </macros>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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6 <expand macro="bio_tools"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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7 <expand macro="requirements"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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8 <expand macro="version_command"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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9 <command detect_errors="exit_code"><![CDATA[
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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10 @CMD@
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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11 ]]></command>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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12 <configfiles>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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13 <configfile name="script_file"><![CDATA[
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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14 @CMD_imports@
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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15 @CMD_read_inputs@
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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16
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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17 #if $method.method == 'pp.binarize'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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18 esc.pp.binarize(
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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19 adata,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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20 copy=False)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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21
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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22 #else if $method.method == 'pp.filter_cells'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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23 esc.pp.filter_cells(
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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24 adata,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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25 #if $method.filter.filter == 'min_counts'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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26 min_counts=$method.filter.min_counts,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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27 #else if $method.filter.filter == 'max_counts'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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28 max_counts=$method.filter.max_counts,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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29 #else if $method.filter.filter == 'min_features'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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30 min_features=$method.filter.min_features,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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31 #else if $method.filter.filter == 'max_features'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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32 max_features=$method.filter.max_features,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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33 #end if
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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34 copy=False)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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35
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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36 #else if $method.method == 'pp.filter_features'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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37 esc.pp.filter_features(
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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38 adata,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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39 #if $method.filter.filter == 'min_counts'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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40 min_counts=$method.filter.min_counts,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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41 #else if $method.filter.filter == 'max_counts'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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42 max_counts=$method.filter.max_counts,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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43 #else if $method.filter.filter == 'min_cells'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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44 min_cells=$method.filter.min_cells,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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45 #else if $method.filter.filter == 'max_cells'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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46 max_cells=$method.filter.max_cells,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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47 #end if
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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48 copy=False)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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49
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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50 #else if $method.method == 'nb_feat_log'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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51 adata.obs['log_nb_features'] = [np.log10(x) for x in adata.obs['nb_features']]
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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52
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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53 #else if $method.method == 'pp.coverage_cells'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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54 esc.pp.coverage_cells(
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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55 adata,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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56 binary=$method.binary,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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57 log=$method.log,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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58 #if $method.threshold
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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59 threshold=$method.threshold,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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60 #end if
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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61 bins=$method.bins,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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62 save='plot.png'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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63 )
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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64 #else if $method.method == 'pp.coverage_features'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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65 esc.pp.coverage_features(
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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66 adata,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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67 binary=$method.binary,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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68 log=$method.log,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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69 #if $method.threshold
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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70 threshold=$method.threshold,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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71 #end if
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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72 bins=$method.bins,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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73 save='plot.png'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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74 )
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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75
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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76 #else if $method.method == 'pp.select_var_feature'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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77 esc.pp.select_var_feature(
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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78 adata,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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79 min_score=$method.min_score,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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80 show=False,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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81 #if $method.nb_features
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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82 nb_features=$method.nb_features
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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83 #end if
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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84 )
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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85
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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86 #else if $method.method == 'pp.cal_var'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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87 esc.pp.cal_var(
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88 adata,
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89 show=True,
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90 color=['b', 'r'],
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91 save='plot.png'
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92 )
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93
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94 #else if $method.method == 'pp.variability_features'
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95 esc.pp.variability_features(
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96 adata,
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97 min_score=$method.min_score,
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98 nb_features=$method.nb_features,
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99 #if $method.log_mode
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100 log='$method.log_mode',
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101 #end if
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102 save='plot.png'
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103 )
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104
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105 #end if
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106 @CMD_anndata_write_outputs@
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107 ]]></configfile>
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108 </configfiles>
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109 <inputs>
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110 <expand macro="inputs_anndata"/>
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111 <conditional name="method">
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112 <param argument="method" type="select" label="Method used for filtering">
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113 <option value="pp.binarize">Binarize count matrix, using 'pp.binarize'</option>
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114 <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of features expressed, using 'pp.filter_cells'</option>
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115 <option value="pp.filter_features">Filter features based on counts and numbers of features expressed, using 'pp.filter_features'</option>
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116 <option value="nb_feat_log">Compute log10 of nb_features</option>
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117 <option value="pp.coverage_cells">Coverage cells: Histogram of the number of open features (in the case of ATAC-seq data) per cell, using 'pp.coverage_cells'</option>
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118 <option value="pp.coverage_features">Coverage features: Distribution of the feature commoness in cells, using 'pp.coverage_features'</option>
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119 <option value="pp.select_var_feature">Select the most variable features, 'pp.select_var_feature'</option>
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120 <option value="pp.cal_var">Show distribution plots of cells sharing features and variability score 'pp.cal_var'</option>
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121 <option value="pp.variability_features">Computes variability score to rank the most variable features across all cells, using 'pp.variability_features'</option>
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122 </param>
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123 <when value="pp.binarize" />
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124 <when value="pp.filter_cells">
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125 <conditional name="filter">
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126 <param argument="filter" type="select" label="Filter" help="Filter mode">
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127 <option value="min_counts">Minimum number of counts</option>
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128 <option value="max_counts">Maximum number of counts</option>
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129 <option value="min_features">Minimum number of features expressed</option>
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130 <option value="max_features">Maximum number of features expressed</option>
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131 </param>
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132 <when value="min_counts">
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133 <param argument="min_counts" type="integer" min="0" value="" label="Minimum counts" help="Minimum number of counts required for a cell to pass filtering"/>
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134 </when>
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135 <when value="max_counts">
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136 <param argument="max_counts" type="integer" min="0" value="" label="Maximum counts" help="Maximum number of counts required for a cell to pass filtering"/>
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137 </when>
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138 <when value="min_features">
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139 <param argument="min_features" type="integer" min="0" value="" label="Minimum features" help="Minimum number of features expressed required for a cell to pass filtering"/>
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140 </when>
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141 <when value="max_features">
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142 <param argument="max_features" type="integer" min="0" value="" label="Maximum features" help="Maximum number of features expressed required for a cell to pass filtering"/>
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143 </when>
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144 </conditional>
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145 </when>
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146 <when value="pp.filter_features">
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147 <conditional name="filter">
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148 <param argument="filter" type="select" label="Filter">
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149 <option value="min_counts">Minimum number of counts</option>
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150 <option value="max_counts">Maximum number of counts</option>
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151 <option value="min_cells">Minimum number of cells expressed</option>
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152 <option value="max_cells">Maximum number of cells expressed</option>
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153 </param>
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154 <when value="min_counts">
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155 <param argument="min_counts" type="integer" min="0" value="" label="Minimum number of counts required for a gene to pass filtering"/>
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156 </when>
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157 <when value="max_counts">
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158 <param argument="max_counts" type="integer" min="0" value="" label="Maximum number of counts required for a gene to pass filtering"/>
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159 </when>
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160 <when value="min_cells">
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161 <param argument="min_cells" type="integer" min="0" value="" label="Minimum number of cells expressed required for a gene to pass filtering"/>
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162 </when>
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163 <when value="max_cells">
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164 <param argument="max_cells" type="integer" min="0" value="" label="Maximum number of cells expressed required for a gene to pass filtering"/>
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165 </when>
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166 </conditional>
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167 </when>
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168 <when value="nb_feat_log" />
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169 <when value="pp.coverage_cells">
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170 <expand macro="coverage_params" />
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171 </when>
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172 <when value="pp.coverage_features">
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173 <expand macro="coverage_params" />
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174 </when>
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175 <when value="pp.select_var_feature">
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176 <param argument="min_score" type="float" min="0" max="1" value="0.5" label="Min score" help="Minimum threshold variability score to retain features" />
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177 <param argument="nb_features" type="integer" min="0" value="" optional="True" label="Number of features" help="Default value is None, if specify it will select a the top most
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178 variable features. If this parameter is larger than the total number of feature, it filters based on the min_score argument." />
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179 </when>
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180 <when value="pp.cal_var" />
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181 <when value="pp.variability_features">
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182 <param name="min_score" type="float" min="0" max="1" value="0.5" label="Minimum score value"/>
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183 <param name="nb_features" type="integer" min="0" value="" label="Number of features"/>
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184 <param name="log_mode" type="select" optional="True" label="Log" help="Log mode">
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185 <option value="log2">Log2</option>
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186 <option value="log10">Log10</option>
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187 </param>
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188 </when>
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189 </conditional>
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190 <expand macro="inputs_common_advanced"/>
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191 </inputs>
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192 <outputs>
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193 <expand macro="anndata_outputs"/>
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194 <data name="out_png" format="png" from_work_dir="plot.png" label="${tool.name} (${method.method}) on ${on_string}">
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195 <filter>method['method'] != 'pp.binarize' and method['method'] != 'pp.filter_cells' and method['method'] != 'pp.filter_features' and method['method'] != 'nb_feat_log' and method['method'] != 'select_var_feature'</filter>
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196 </data>
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197 </outputs>
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198 <tests>
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199 <test expect_num_outputs="1">
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200 <!-- pp.binarize -->
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201 <param name="adata" value="krumsiek11.h5ad" />
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202 <conditional name="method">
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203 <param name="method" value="pp.binarize"/>
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204 </conditional>
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205 <output name="anndata_out" file="krumsiek11.pp.binarize.h5ad" ftype="h5ad" compare="sim_size"/>
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206 </test>
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207 <test expect_num_outputs="2">
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208 <!-- pp.filter_cells -->
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209 <param name="adata" value="krumsiek11.h5ad" />
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210 <conditional name="method">
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211 <param name="method" value="pp.filter_cells"/>
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212 <conditional name="filter">
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213 <param name="filter" value="min_features"/>
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214 <param name="min_features" value="10"/>
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215 </conditional>
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216 </conditional>
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217 <section name="advanced_common">
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218 <param name="show_log" value="true" />
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219 </section>
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220 <assert_stdout>
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221 <has_text_matching expression="395 × 11"/>
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222 </assert_stdout>
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223 <output name="hidden_output">
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224 <assert_contents>
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225 <has_text_matching expression="esc.pp.filter_cells"/>
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226 <has_text_matching expression="min_features=10"/>
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227 </assert_contents>
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228 </output>
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229 <output name="anndata_out" file="krumsiek11.pp.filter_cells.min_features.h5ad" ftype="h5ad" compare="sim_size"/>
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230 </test>
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231 <test expect_num_outputs="2">
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232 <!-- pp.filter_features -->
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233 <param name="adata" value="krumsiek11.h5ad" />
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234 <conditional name="method">
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235 <param name="method" value="pp.filter_features"/>
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236 <conditional name="filter">
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237 <param name="filter" value="min_cells"/>
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238 <param name="min_cells" value="600"/>
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239 </conditional>
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240 </conditional>
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241 <section name="advanced_common">
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242 <param name="show_log" value="true" />
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243 </section>
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244 <assert_stdout>
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245 <has_text_matching expression="640 × 2"/>
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246 </assert_stdout>
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247 <output name="hidden_output">
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248 <assert_contents>
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249 <has_text_matching expression="esc.pp.filter_features"/>
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250 <has_text_matching expression="min_cells=600"/>
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251 </assert_contents>
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252 </output>
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253 <output name="anndata_out" file="krumsiek11.pp.filter_features.min_cells.h5ad" ftype="h5ad" compare="sim_size"/>
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254 </test>
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255 <test expect_num_outputs="1">
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256 <!-- nb_feat_log -->
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257 <param name="adata" value="krumsiek11.pp.filter_cells.min_features.h5ad" />
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258 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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259 <param name="method" value="nb_feat_log"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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260 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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261 <assert_stdout>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
262 <has_text_matching expression="log_nb_features"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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263 <has_text_matching expression="nb_features"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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264 </assert_stdout>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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265 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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266 <test expect_num_outputs="3">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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267 <!-- pp.select_var_feature -->
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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268 <param name="adata" value="krumsiek11.h5ad" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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269 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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270 <param name="method" value="pp.select_var_feature"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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271 <param name="min_score" value="0.6"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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272 <param name="nb_features" value="10"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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273 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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274 <section name="advanced_common">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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275 <param name="show_log" value="true" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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276 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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277 <assert_stdout>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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278 <has_text_matching expression="prop_shared_cells"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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279 <has_text_matching expression="variability_score"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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280 </assert_stdout>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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281 <output name="hidden_output">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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282 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
283 <has_text_matching expression="esc.pp.select_var_feature"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
284 <has_text_matching expression="adata"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
285 <has_text_matching expression="min_score=0.6"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
286 <has_text_matching expression="nb_features=10"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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287 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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288 </output>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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289 <output name="anndata_out" file="krumsiek11.pp.select_var_feature.h5ad" ftype="h5ad" compare="sim_size"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
290 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
291 <test expect_num_outputs="3">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
292 <!-- pp.cal_var -->
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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293 <param name="adata" value="krumsiek11.h5ad" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
294 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
295 <param name="method" value="pp.cal_var"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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296 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
297 <section name="advanced_common">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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298 <param name="show_log" value="true" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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299 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
300 <output name="hidden_output">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
301 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
302 <has_text_matching expression="esc.pp.cal_var"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
303 <has_text_matching expression="adata"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
304 <has_text_matching expression="plot.png"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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305 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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306 </output>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
307 <output name="anndata_out" file="krumsiek11.pp.cal_var.h5ad" ftype="h5ad" compare="sim_size"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
308 <output name="out_png" file="krumsiek11.pp.cal_var.png" ftype="png" compare="sim_size"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
309 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
310 <test expect_num_outputs="3">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
311 <!-- pp.coverage_cells -->
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
312 <param name="adata" value="krumsiek11.h5ad" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
313 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
314 <param name="method" value="pp.coverage_cells"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
315 <param name="threshold" value="3.0" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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316 <param name="binary" value="True" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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317 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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318 <section name="advanced_common">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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319 <param name="show_log" value="true" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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320 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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321 <output name="hidden_output">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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322 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
323 <has_text_matching expression="esc.pp.coverage_cells"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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324 <has_text_matching expression="adata"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
325 <has_text_matching expression="threshold=3.0"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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326 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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327 </output>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
328 <output name="anndata_out" file="krumsiek11.pp.coverage_cells.h5ad" ftype="h5ad" compare="sim_size"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
329 <output name="out_png" file="krumsiek11.pp.coverage_cells.png" ftype="png" compare="sim_size"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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330 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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331 <test expect_num_outputs="3">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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332 <!-- pp.coverage_features -->
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
333 <param name="adata" value="krumsiek11.h5ad" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
334 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
335 <param name="method" value="pp.coverage_features"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
336 <param name="threshold" value="100" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
337 <param name="binary" value="True" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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338 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
339 <section name="advanced_common">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
340 <param name="show_log" value="true" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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341 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
342 <output name="hidden_output">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
343 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
344 <has_text_matching expression="esc.pp.coverage_features"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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345 <has_text_matching expression="adata"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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346 <has_text_matching expression="threshold=100"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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347 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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348 </output>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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349 <output name="anndata_out" file="krumsiek11.pp.coverage_features.h5ad" ftype="h5ad" compare="sim_size"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
350 <output name="out_png" file="krumsiek11.pp.coverage_features.png" ftype="png" compare="sim_size"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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351 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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352 <test expect_num_outputs="3">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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353 <!-- pp.coverage_features -->
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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354 <param name="adata" value="krumsiek11.h5ad" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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355 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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356 <param name="method" value="pp.variability_features"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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357 <param name="min_score" value="0.75" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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358 <param name="nb_features" value="8" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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359 <param name="log" value="log10" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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360 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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361 <section name="advanced_common">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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362 <param name="show_log" value="true" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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363 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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364 <output name="hidden_output">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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365 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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366 <has_text_matching expression="esc.pp.variability_features"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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367 <has_text_matching expression="adata"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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368 <has_text_matching expression="min_score=0.75"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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369 <has_text_matching expression="nb_features=8"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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370 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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371 </output>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
372 <output name="anndata_out" file="krumsiek11.pp.variability_features.h5ad" ftype="h5ad" compare="sim_size"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
373 <output name="out_png" file="krumsiek11.pp.variability_features.png" ftype="png" compare="sim_size"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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374 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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375 </tests>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
376 <help><![CDATA[
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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377
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
378 convert the count matrix into a binary matrix (`pp.binarize`)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
379 ============================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
380 convert the count matrix into a binary matrix
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
381
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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382 More details on the `episcanpy documentation
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
383 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.binarize.html>`__
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
384
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
385 Filter cells outliers based on counts and numbers of features expressed (`pp.filter_cells`)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
386 ============================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
387 For instance, only keep cells with at least *min_counts* counts or *min_features* genes expressed.
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
388 This is to filter measurement outliers, i.e. "unreliable" observations.
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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389
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
390 Only provide one of the optional parameters *min_counts*, *min_features*, *max_counts*, *max_features* per call.
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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391
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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392 More details on the `episcanpy documentation
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
393 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.filter_cells.html>`__
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
394
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
395 Filter features based on number of cells or counts (`pp.filter_features`)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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396 ========================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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397 Keep features that have at least *min_counts* counts or are expressed in at least *min_cells* cells or
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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398 have at most *max_counts* counts or are expressed in at most *max_cells* cells.
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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399
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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400 Only provide one of the optional parameters *min_counts*, *min_cells*, *max_counts*, *max_cells* per call.
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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401
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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402 More details on the `episcanpy documentation
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
403 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.filter_features.html>`__
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
404
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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405 Histogram of the number of open features (`pp.coverage_cells`)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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406 ========================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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407 Histogram of the number of open features (in the case of ATAC-seq data) per cell.
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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408
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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409 More details on the `episcanpy documentation
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
410 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.coverage_cells.html>`__
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
411
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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412 Distribution of the feature commoness in cells (`pp.coverage_features`)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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413 ========================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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414 Display how often a feature is measured as open (for ATAC-seq). Distribution of the feature commoness in cells.
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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415
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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416 More details on the `episcanpy documentation
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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417 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.coverage_features.html>`__
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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418
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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419 Selects the most variable features according to either a specified number of features or minimum variance score (`pp.select_var_feature`)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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420 =========================================================================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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421
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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422 This function computes a variability score to rank the most variable features across all cells. Then it selects the most variable features according to either a specified number of features (nb_features) or a minimum variance score (min_score).
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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423
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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424 More details on the `episcanpy documentation
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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425 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.select_var_feature.html>`__
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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426
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
427 Distribution of cells sharing features and variability score (`pp.cal_var`)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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428 =============================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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429
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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430 Show distribution plots of cells sharing features and variability score.
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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431
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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432 More details on the `episcanpy documentation
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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433 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.cal_var.html>`__
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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434
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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435 Compute a variability score to rank the most variable features across all cells (`pp.variability_features`)
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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436 ============================================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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437
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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438 This function computes a variability score to rank the most variable features across all cells. Then it selects the most variable features according to either a specified number of features (nb_features) or a minimum variance score (min_score).
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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439
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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440 More details on the `episcanpy documentation
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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441 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.variability_features.html>`__
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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442 ]]></help>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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443 <expand macro="citations"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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444 </tool>