Mercurial > repos > iuc > episcanpy_preprocess

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
author iuc
date Sat, 22 Apr 2023 12:12:40 +0000
parents 307f05e02a03
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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
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10 @CMD@
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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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
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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
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14 @CMD_imports@
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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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
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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
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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
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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 $method.filter.filter == 'max_cells'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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46 max_cells=$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
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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
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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
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53 #else if $method.method == 'pp.coverage_cells'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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54 esc.pp.coverage_cells(
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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55 adata,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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56 binary=$method.binary,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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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
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58 #if $method.threshold
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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59 threshold=$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
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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
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64 #else if $method.method == 'pp.coverage_features'
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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65 esc.pp.coverage_features(
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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66 adata,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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67 binary=$method.binary,
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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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
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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
1
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105 #else if $method.method == 'tl.find_genes'
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106 esc.tl.find_genes(
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107 adata,
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108 gtf_file='$method.find_genes_gtf_file',
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109 key_added='$method.find_genes_key_added',
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110 upstream=$method.find_genes_upstream,
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111 feature_type='$method.find_genes_feature_type',
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112 annotation='$method.find_genes_annotation',
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113 raw=$method.find_genes_raw)
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114
0
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115 #end if
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116 @CMD_anndata_write_outputs@
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117 ]]></configfile>
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118 </configfiles>
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119 <inputs>
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120 <expand macro="inputs_anndata"/>
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121 <conditional name="method">
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122 <param argument="method" type="select" label="Method used for filtering">
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123 <option value="pp.binarize">Binarize count matrix, using 'pp.binarize'</option>
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124 <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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125 <option value="pp.filter_features">Filter features based on counts and numbers of features expressed, using 'pp.filter_features'</option>
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126 <option value="nb_feat_log">Compute log10 of nb_features</option>
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127 <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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128 <option value="pp.coverage_features">Coverage features: Distribution of the feature commoness in cells, using 'pp.coverage_features'</option>
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129 <option value="pp.select_var_feature">Select the most variable features, 'pp.select_var_feature'</option>
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130 <option value="pp.cal_var">Show distribution plots of cells sharing features and variability score 'pp.cal_var'</option>
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131 <option value="pp.variability_features">Computes variability score to rank the most variable features across all cells, using 'pp.variability_features'</option>
1
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132 <option value="tl.find_genes">Embedding: Find genes and add annotations, using 'pp.find_genes'</option>
0
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133 </param>
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134 <when value="pp.binarize" />
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135 <when value="pp.filter_cells">
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136 <conditional name="filter">
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137 <param argument="filter" type="select" label="Filter" help="Filter mode">
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138 <option value="min_counts">Minimum number of counts</option>
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139 <option value="max_counts">Maximum number of counts</option>
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140 <option value="min_features">Minimum number of features expressed</option>
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141 <option value="max_features">Maximum number of features expressed</option>
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142 </param>
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143 <when value="min_counts">
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144 <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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145 </when>
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146 <when value="max_counts">
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147 <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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148 </when>
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149 <when value="min_features">
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150 <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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151 </when>
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152 <when value="max_features">
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153 <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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154 </when>
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155 </conditional>
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156 </when>
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157 <when value="pp.filter_features">
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158 <conditional name="filter">
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159 <param argument="filter" type="select" label="Filter">
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160 <option value="min_counts">Minimum number of counts</option>
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161 <option value="max_counts">Maximum number of counts</option>
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162 <option value="min_cells">Minimum number of cells expressed</option>
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163 <option value="max_cells">Maximum number of cells expressed</option>
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164 </param>
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165 <when value="min_counts">
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166 <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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167 </when>
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168 <when value="max_counts">
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169 <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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170 </when>
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171 <when value="min_cells">
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172 <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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173 </when>
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174 <when value="max_cells">
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175 <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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176 </when>
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177 </conditional>
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178 </when>
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179 <when value="nb_feat_log" />
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180 <when value="pp.coverage_cells">
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181 <expand macro="coverage_params" />
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182 </when>
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183 <when value="pp.coverage_features">
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184 <expand macro="coverage_params" />
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185 </when>
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186 <when value="pp.select_var_feature">
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187 <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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188 <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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189 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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190 </when>
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191 <when value="pp.cal_var" />
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192 <when value="pp.variability_features">
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193 <param name="min_score" type="float" min="0" max="1" value="0.5" label="Minimum score value"/>
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194 <param name="nb_features" type="integer" min="0" value="" label="Number of features"/>
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195 <param name="log_mode" type="select" optional="True" label="Log" help="Log mode">
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196 <option value="log2">Log2</option>
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197 <option value="log10">Log10</option>
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198 </param>
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199 </when>
1
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200 <when value="tl.find_genes">
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201 <param name="find_genes_gtf_file" type="data" format="gtf" label="Annotation GTF file" help="(gtf_file)"/>
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202 <param name="find_genes_key_added" value="transcript_annotation" type="text" label="Key added" help="(key_added)">
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203 <sanitizer invalid_char="">
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204 <valid initial="string.letters,string.digits">
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205 <add value="_" />
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206 <add value="-" />
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207 <add value="." />
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208 <add value=" " />
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209 <add value="," />
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210 </valid>
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211 </sanitizer>
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212 <validator type="regex">[0-9a-zA-Z_., -]+</validator>
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213 </param>
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214 <param name="find_genes_upstream" value="2000" min="0" type="integer" label="Upstream" help="(upstream)"/>
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215 <param name="find_genes_feature_type" value="transcript" type="text" label="Feature type" help="(feature_type)">
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216 <sanitizer invalid_char="">
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217 <valid initial="string.letters,string.digits">
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218 <add value="_" />
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219 <add value="-" />
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220 <add value="." />
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221 <add value=" " />
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222 <add value="," />
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223 </valid>
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224 </sanitizer>
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225 <validator type="regex">[0-9a-zA-Z_., -]+</validator>
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226 </param>
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227 <param name="find_genes_annotation" value="HAVANA" type="text" label="Annotation" help="(annotation)">
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228 <sanitizer invalid_char="">
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229 <valid initial="string.letters,string.digits">
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230 <add value="_" />
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231 <add value="-" />
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232 <add value="." />
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233 <add value=" " />
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234 <add value="," />
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235 </valid>
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236 </sanitizer>
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237 <validator type="regex">[0-9a-zA-Z_., -]+</validator>
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238 </param>
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239 <param name="find_genes_raw" type="select" label="Raw?" help="(raw)">
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240 <option value="True">True</option>
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241 <option value="False" selected="true">False</option>
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242 </param>
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243 </when>
0
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244 </conditional>
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245 <expand macro="inputs_common_advanced"/>
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246 </inputs>
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247 <outputs>
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248 <expand macro="anndata_outputs"/>
1
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249 <data name="out_png" format="png" from_work_dir="plot.png" label="${tool.name} (${method.method}) plot on ${on_string}">
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250 <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'] != 'pp.select_var_feature' and method['method'] !='tl.find_genes'</filter>
0
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251 </data>
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252 </outputs>
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253 <tests>
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254 <test expect_num_outputs="1">
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255 <!-- pp.binarize -->
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256 <param name="adata" value="krumsiek11.h5ad" />
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257 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
258 <param name="method" value="pp.binarize"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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259 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
260 <output name="anndata_out" file="krumsiek11.pp.binarize.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
261 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
262 <test expect_num_outputs="2">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
263 <!-- pp.filter_cells -->
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
264 <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
265 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
266 <param name="method" value="pp.filter_cells"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
267 <conditional name="filter">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
268 <param name="filter" value="min_features"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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269 <param name="min_features" value="10"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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270 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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271 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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272 <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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273 <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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274 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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275 <assert_stdout>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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276 <has_text_matching expression="395 × 11"/>
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
parents:
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278 <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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279 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
280 <has_text_matching expression="esc.pp.filter_cells"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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281 <has_text_matching expression="min_features=10"/>
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
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283 </output>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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284 <output name="anndata_out" file="krumsiek11.pp.filter_cells.min_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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285 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
286 <test expect_num_outputs="2">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
287 <!-- 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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diff changeset
288 <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
289 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
290 <param name="method" value="pp.filter_features"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
291 <conditional name="filter">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
292 <param name="filter" value="min_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
293 <param name="min_cells" value="600"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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294 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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295 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
296 <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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297 <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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298 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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299 <assert_stdout>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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300 <has_text_matching expression="640 × 2"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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301 </assert_stdout>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
302 <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
303 <assert_contents>
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="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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diff changeset
305 <has_text_matching expression="min_cells=600"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
306 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
307 </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
308 <output name="anndata_out" file="krumsiek11.pp.filter_features.min_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
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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
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diff changeset
310 <test expect_num_outputs="1">
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 <!-- 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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diff changeset
312 <param name="adata" value="krumsiek11.pp.filter_cells.min_features.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="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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315 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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316 <assert_stdout>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
317 <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
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318 <has_text_matching expression="nb_features"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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319 </assert_stdout>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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320 </test>
1
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
321 <test expect_num_outputs="2">
0
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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322 <!-- 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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323 <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
324 <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
325 <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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diff changeset
326 <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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diff changeset
327 <param name="nb_features" value="10"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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328 </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
329 <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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330 <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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331 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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332 <assert_stdout>
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 <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
parents:
diff changeset
334 <has_text_matching expression="variability_score"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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335 </assert_stdout>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
336 <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
337 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
338 <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
339 <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
340 <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
341 <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
parents:
diff changeset
342 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
343 </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
344 <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
parents:
diff changeset
345 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
346 <test expect_num_outputs="3">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
347 <!-- pp.cal_var -->
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
348 <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
349 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
350 <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
parents:
diff changeset
351 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
352 <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
353 <param name="show_log" value="true" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
354 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
355 <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
356 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
357 <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
358 <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
359 <has_text_matching expression="plot.png"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
360 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
361 </output>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
362 <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
363 <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
parents:
diff changeset
364 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
365 <test expect_num_outputs="3">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
366 <!-- pp.coverage_cells -->
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
367 <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
368 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
369 <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
370 <param name="threshold" value="3.0" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
371 <param name="binary" value="True" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
372 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
373 <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
374 <param name="show_log" value="true" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
375 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
376 <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
377 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
378 <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
parents:
diff changeset
379 <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
380 <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
parents:
diff changeset
381 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
382 </output>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
383 <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
384 <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
parents:
diff changeset
385 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
386 <test expect_num_outputs="3">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
387 <!-- pp.coverage_features -->
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
388 <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
389 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
390 <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
391 <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
392 <param name="binary" value="True" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
393 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
394 <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
395 <param name="show_log" value="true" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
396 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
397 <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
398 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
399 <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
parents:
diff changeset
400 <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
401 <has_text_matching expression="threshold=100"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
402 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
403 </output>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
404 <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
parents:
diff changeset
405 <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
parents:
diff changeset
406 </test>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
407 <test expect_num_outputs="3">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
408 <!-- pp.coverage_features -->
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
409 <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
410 <conditional name="method">
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
411 <param name="method" value="pp.variability_features"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
412 <param name="min_score" value="0.75" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
413 <param name="nb_features" value="8" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
414 <param name="log" value="log10" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
415 </conditional>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
416 <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
417 <param name="show_log" value="true" />
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
418 </section>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
419 <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
420 <assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
421 <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
parents:
diff changeset
422 <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
423 <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
parents:
diff changeset
424 <has_text_matching expression="nb_features=8"/>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
425 </assert_contents>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
426 </output>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
427 <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
parents:
diff changeset
428 <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
iuc
parents:
diff changeset
429 </test>
1
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
430 <test expect_num_outputs="2">
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
431 <!-- tl.find_genes -->
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
432 <param name="adata" value="chrY.h5ad" />
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
433 <conditional name="method">
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
434 <param name="method" value="tl.find_genes"/>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
435 <param name="find_genes_gtf_file" value="chrY.gtf"/>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
436 <param name="find_genes_key_added" value="transcript_annotation"/>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
437 <param name="find_genes_upstream" value="2000"/>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
438 <param name="find_genes_feature_type" value="transcript"/>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
439 <param name="find_genes_annotation" value="HAVANA"/>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
440 <param name="find_genes_raw" value="False"/>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
441 </conditional>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
442 <section name="advanced_common">
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
443 <param name="show_log" value="true" />
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
444 </section>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
445 <output name="anndata_out" file="chrY_with_transcript_annotation.h5ad" ftype="h5ad" compare="sim_size">
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
446 <assert_contents>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
447 <has_h5_keys keys="var" />
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
448 </assert_contents>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
449 </output>
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
450 </test>
0
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
451 </tests>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
452 <help><![CDATA[
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
453
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
454 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
455 ============================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
456 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
parents:
diff changeset
457
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
458 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
459 <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
parents:
diff changeset
460
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
461 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
462 ============================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
463 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
parents:
diff changeset
464 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
iuc
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diff changeset
465
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
466 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
iuc
parents:
diff changeset
467
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
468 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
469 <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
470
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
471 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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diff changeset
472 ========================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
473 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
iuc
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diff changeset
474 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
parents:
diff changeset
475
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
476 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
parents:
diff changeset
477
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
478 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
479 <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
parents:
diff changeset
480
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
481 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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482 ========================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
483 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
iuc
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diff changeset
484
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
485 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
486 <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
487
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
488 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
iuc
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diff changeset
489 ========================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
490 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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diff changeset
491
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
492 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
493 <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
iuc
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diff changeset
494
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
495 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
iuc
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diff changeset
496 =========================================================================================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
497
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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diff changeset
498 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
iuc
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diff changeset
499
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
500 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
501 <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
iuc
parents:
diff changeset
502
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
503 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
iuc
parents:
diff changeset
504 =============================================================================
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
505 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
iuc
parents:
diff changeset
506
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
507 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
508 <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
iuc
parents:
diff changeset
509
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff changeset
510 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
iuc
parents:
diff changeset
511 ============================================================================================================
1
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
512 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).
0
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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diff changeset
513
1
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
iuc
parents: 0
diff changeset
514 Find and add gene annotations (`tl.find_genes`)
ed9b88a259f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
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515 ========================================================================================
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516 This function adds a gene annotation to an AnnData (h5ad) file from annotations file (.annotation.gtf).
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307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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517
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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518 More details on the `episcanpy documentation
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519 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.variability_features.html>`__
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520 ]]></help>
307f05e02a03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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521 <expand macro="citations"/>
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522 </tool>