Mercurial > repos > ebi-gxa > scanpy_find_markers
annotate scanpy-find-markers.xml @ 25:e2f004c3b2b3 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 85dcbc74a856bd55865bd372601de39af72dfd29-dirty"
author | ebi-gxa |
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date | Tue, 28 Sep 2021 17:44:18 +0000 |
parents | a6a896082cd7 |
children | a57c0538e56b |
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c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <?xml version="1.0" encoding="utf-8"?> |
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a6a896082cd7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 858a2398f1dbbd60110867c593c237358c794615-dirty"
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2 <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> |
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c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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3 <description>to find differentially expressed genes between groups</description> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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4 <macros> |
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71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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5 <import>scanpy_macros2.xml</import> |
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c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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6 </macros> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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7 <expand macro="requirements"/> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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8 <command detect_errors="exit_code"><![CDATA[ |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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9 ln -s '${input_obj_file}' input.h5 && |
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71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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10 PYTHONIOENCODING=utf-8 scanpy-find-markers |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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11 #if $output_markers |
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cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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12 --save diffexp.tsv |
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71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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13 #end if |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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14 --n-genes '${n_genes}' |
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f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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15 #if $groupby_file |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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16 #set f = open($groupby_file.__str__) |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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17 #set groupby = f.read().strip() |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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18 #silent f.close |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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19 #else |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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20 #set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name')) |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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21 #end if |
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71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
ebi-gxa
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22 --groupby '${groupby}' |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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23 #if $settings.default == "false" |
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1670af5eee46
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 0fc0cc467014e750dbaa6c47b528b25af0bdc0c4-dirty"
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24 #if $settings.key_added |
1670af5eee46
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 0fc0cc467014e750dbaa6c47b528b25af0bdc0c4-dirty"
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25 #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__) |
1670af5eee46
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 0fc0cc467014e750dbaa6c47b528b25af0bdc0c4-dirty"
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26 --key-added '${key_added}' |
1670af5eee46
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 0fc0cc467014e750dbaa6c47b528b25af0bdc0c4-dirty"
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27 #end if |
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71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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28 --method '${settings.method}' |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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29 ${settings.use_raw} |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
ebi-gxa
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30 ${settings.rankby_abs} |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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31 #if $settings.groups |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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32 --groups '${settings.groups}' |
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c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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33 #end if |
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71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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34 --reference '${settings.reference}' |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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35 --filter-params 'min_in_group_fraction:${settings.min_in_group_fraction},max_out_group_fraction:${settings.max_out_group_fraction},min_fold_change:${settings.min_fold_change}' |
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615a46c220f0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit dc04b063913e5d8ae360b51b62adde47bc1ddac7-dirty"
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36 $settings.pts $settings.tie_correct |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
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37 #end if |
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71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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38 @INPUT_OPTS@ |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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39 @OUTPUT_OPTS@ |
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c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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40 ]]></command> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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41 |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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42 <inputs> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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43 <expand macro="input_object_params"/> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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44 <expand macro="output_object_params"/> |
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cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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45 <param name="output_markers" type="boolean" checked="true" label="Output markers table in tsv format"/> |
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c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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46 <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/> |
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71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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47 <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/> |
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f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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48 <param name="groupby_file" argument="--groupby" type="data" format="txt,tsv" optional="true" |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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49 label="File with groupby. Overrides the groupby setting"/> |
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c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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50 <conditional name="settings"> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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51 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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52 <when value="true"/> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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53 <when value="false"> |
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cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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54 <param name="key_added" argument="--key-added" type="text" optional="true" |
cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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55 label="The key in adata.uns information is saved to. If included, the keyword 'GROUPBY' will be substituted with the value of the groupby setting."/> |
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c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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56 <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes"> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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57 <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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58 <option value="t-test">t-test</option> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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59 <option value="wilcoxon">wilcoxon test, currently broken don't use</option> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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60 <option value="logreg">logistic regression</option> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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61 </param> |
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71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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62 <param name="use_raw" type="boolean" truevalue="--use-raw" falsevalue="--no-raw" checked="true" |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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63 label="Use raw attribute if present"/> |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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64 <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false" |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
ebi-gxa
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65 label="Rank by absolute value of the scores instead of the scores"/> |
0
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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66 <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/> |
1
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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67 <param name="reference" argument="--reference" type="text" value="rest" label="If 'rest', compare to the union of the rest of the group/cluster. If a group identifier, compare to that group"/> |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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68 <param name="min_in_group_fraction" type="float" min="0.0" max="1.0" value="0.25" label="Minimum in-group fraction" |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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69 help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/> |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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70 <param name="max_out_group_fraction" type="float" min="0.0" max="1.0" value="0.5" label="Maximum out-group fraction" |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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diff
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71 help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/> |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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72 <param name="min_fold_change" type="float" value="2" label="Minimum fold change" |
71668dd2d47b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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73 help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/> |
12
f6291dbb3afc
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
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74 <param name="pts" argument="--pts" type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" /> |
f6291dbb3afc
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
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75 <param name="tie_correct" argument="--tie-correct" type="boolean" checked="false" label="Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'." truevalue="--tie-correct" falsevalue=""/> |
0
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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76 </when> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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77 </conditional> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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78 </inputs> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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79 |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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80 <outputs> |
5
74100c9351bc
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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81 <expand macro="output_data_obj" description="Marker genes"/> |
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cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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82 <data name="output_tsv" format="tabular" from_work_dir="diffexp.tsv" label="${tool.name} on ${on_string}: Marker table"> |
0
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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83 <filter>output_markers</filter> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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84 </data> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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85 </outputs> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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86 |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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87 <tests> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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88 <test> |
15
cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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89 <param name="input_obj_file" value="louvain_1.0"/> |
0
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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90 <param name="input_format" value="anndata"/> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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91 <param name="output_format" value="anndata"/> |
15
cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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92 <param name="output_tsv" value="true"/> |
0
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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93 <param name="n_genes" value="50"/> |
15
cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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94 <param name="output_markers" value="true"/> |
0
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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95 <param name="default" value="false"/> |
15
cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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96 <param name="groupby" value="INPUT_OBJ"/> |
cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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97 <param name="key_added" value="GROUPBY_marker"/> |
0
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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98 <param name="method" value="t-test_overestim_var"/> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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99 <param name="rankby_abs" value="false"/> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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100 <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/> |
15
cc776860fae1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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101 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> |
0
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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102 </test> |
17
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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103 <test> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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104 <param name="input_obj_file" value="louvain_1.0"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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105 <param name="input_format" value="anndata"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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106 <param name="output_format" value="anndata"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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107 <param name="output_tsv" value="true"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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108 <param name="n_genes" value="50"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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109 <param name="output_markers" value="true"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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110 <param name="default" value="false"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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111 <param name="groupby_file" value="groupby.txt"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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112 <param name="key_added" value="GROUPBY_marker"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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113 <param name="method" value="t-test_overestim_var"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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114 <param name="rankby_abs" value="false"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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115 <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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116 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> |
f04dd4e5b6a7
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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117 </test> |
0
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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118 </tests> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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119 |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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120 <help><![CDATA[ |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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121 ============================================================= |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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122 Rank genes for characterizing groups (`tl.rank_genes_groups`) |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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123 ============================================================= |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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124 |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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125 Rank genes for characterizing groups. |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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126 |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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127 @HELP@ |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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128 |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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129 @VERSION_HISTORY@ |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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130 ]]></help> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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131 <expand macro="citations"/> |
c608fd80ec15
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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132 </tool> |