Mercurial > repos > iuc > scanpy_filter
annotate filter.xml @ 15:aa0059118fb9 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
author | iuc |
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date | Wed, 31 Jul 2024 18:10:52 +0000 |
parents | d636ce5cde16 |
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rev | line source |
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12
a03ff8633507
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
parents:
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diff
changeset
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1 <tool id="scanpy_filter" name="Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@"> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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2 <description>with scanpy</description> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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3 <macros> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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5 </macros> |
11
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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6 <expand macro="bio_tools"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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7 <expand macro="requirements"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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8 <expand macro="version_command"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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9 <command detect_errors="exit_code"><![CDATA[ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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10 @CMD@ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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11 ]]></command> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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12 <configfiles> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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13 <configfile name="script_file"><![CDATA[ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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14 @CMD_imports@ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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15 @CMD_read_inputs@ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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16 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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17 #if $method.method == 'pp.filter_cells' |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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changeset
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18 sc.pp.filter_cells( |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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19 adata, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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20 #if $method.filter.filter == 'min_counts' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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21 min_counts=$method.filter.min_counts, |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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changeset
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22 #else if $method.filter.filter == 'max_counts' |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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23 max_counts=$method.filter.max_counts, |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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24 #else if $method.filter.filter == 'min_genes' |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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25 min_genes=$method.filter.min_genes, |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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26 #else if $method.filter.filter == 'max_genes' |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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27 max_genes=$method.filter.max_genes, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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28 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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29 copy=False) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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30 |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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changeset
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31 #else if $method.method == 'pp.filter_genes' |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
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32 sc.pp.filter_genes( |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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33 adata, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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34 #if $method.filter.filter == 'min_counts' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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35 min_counts=$method.filter.min_counts, |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
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36 #else if $method.filter.filter == 'max_counts' |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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37 max_counts=$method.filter.max_counts, |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
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38 #else if $method.filter.filter == 'min_cells' |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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39 min_cells=$method.filter.min_cells, |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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40 #else if $method.filter.filter == 'max_cells' |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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41 max_cells=$method.filter.max_cells, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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42 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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43 copy=False) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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44 |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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45 #else if $method.method == 'tl.filter_rank_genes_groups' |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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46 sc.tl.filter_rank_genes_groups( |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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47 adata, |
12
a03ff8633507
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
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48 #if $method.key |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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49 key='$method.key', |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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50 #end if |
12
a03ff8633507
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
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51 #if $method.groupby |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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52 groupby='$method.groupby', |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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53 #end if |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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54 use_raw=$method.use_raw, |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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55 key_added='$method.key_added', |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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56 min_in_group_fraction=$method.min_in_group_fraction, |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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57 max_out_group_fraction=$method.max_out_group_fraction, |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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58 min_fold_change=$method.min_fold_change) |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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59 |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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60 #else if $method.method == "pp.highly_variable_genes" |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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61 sc.pp.highly_variable_genes( |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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62 adata=adata, |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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63 flavor='$method.flavor.flavor', |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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64 #if $method.flavor.flavor == 'seurat' |
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a03ff8633507
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
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65 min_mean=$method.flavor.min_mean, |
a03ff8633507
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
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66 max_mean=$method.flavor.max_mean, |
a03ff8633507
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
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67 min_disp=$method.flavor.min_disp, |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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68 #if str($method.flavor.max_disp) != '' |
12
a03ff8633507
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
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69 max_disp=$method.flavor.max_disp, |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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70 #end if |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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71 #else if $method.flavor.flavor == 'cell_ranger' |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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72 n_top_genes=$method.flavor.n_top_genes, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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73 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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74 n_bins=$method.n_bins, |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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75 subset=$method.subset, |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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76 inplace=True) |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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77 |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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78 #else if $method.method == 'pp.subsample' |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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79 sc.pp.subsample( |
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80 data=adata, |
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81 #if $method.type.type == 'fraction' |
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82 fraction=$method.type.fraction, |
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83 #else if $method.type.type == 'n_obs' |
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84 n_obs=$method.type.n_obs, |
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85 #end if |
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86 random_state=$method.random_state, |
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87 copy=False) |
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88 |
1
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89 #else if $method.method == "pp.downsample_counts" |
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90 sc.pp.downsample_counts( |
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91 adata=adata, |
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92 #if str($method.counts_per_cell) != '' |
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93 counts_per_cell=$method.counts_per_cell, |
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94 #end if |
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95 #if str($method.total_counts) != '' |
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96 total_counts=$method.total_counts, |
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97 #end if |
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98 random_state=$method.random_state, |
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99 replace=$method.replace, |
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100 copy=False) |
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101 |
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102 #else if $method.method == "filter_marker" |
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103 |
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104 #if $method.layer_selection.use_raw == 'False': |
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105 adata.X = adata.layers['$method.layer_selection.layer'] |
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106 #end if |
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107 |
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108 def check_marker(adata, group, gene, thresh_mean, thresh_frac, groupby): |
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109 filtered_data = adata[adata.obs[groupby] == group, adata.var_names == gene] |
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110 mean_expression = np.mean(filtered_data.X) |
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111 frac_cell_mean_expression = len(filtered_data.X[filtered_data.X > mean_expression]) / filtered_data.n_obs |
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112 if ( mean_expression > thresh_mean and frac_cell_mean_expression >= thresh_frac ): |
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113 return(True) |
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114 return(False) |
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115 |
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116 header='infer' |
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117 |
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118 #if $method.header == 'not_included': |
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119 header=None |
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120 #end if |
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121 |
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122 marker_list={key: list(value.values()) for key, value in pd.read_csv('$method.markerfile', sep='\t', index_col=0, header=header).to_dict(orient='index').items()} |
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123 |
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124 for key, value in marker_list.items(): |
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125 marker_list[key] = [x for x in value if check_marker(adata, key, x, $method.thresh_mean, $method.thresh_frac, '$method.groupby')] |
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126 |
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127 # Find the maximum length of lists |
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128 max_len = max(len(lst) for lst in marker_list.values()) |
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129 |
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130 # Fill smaller lists with empty values |
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131 for key, value in marker_list.items(): |
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132 marker_list[key] = value + [''] * (max_len - len(value)) |
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133 |
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134 df = pd.DataFrame(marker_list).T |
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135 df.to_csv('marker.tsv', sep='\t', index=True) |
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136 #end if |
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137 |
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138 @CMD_anndata_write_outputs@ |
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139 ]]></configfile> |
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140 </configfiles> |
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141 <inputs> |
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142 <expand macro="inputs_anndata"/> |
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143 <conditional name="method"> |
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144 <param argument="method" type="select" label="Method used for filtering"> |
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145 <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using 'pp.filter_cells'</option> |
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146 <option value="pp.filter_genes">Filter genes based on number of cells or counts, using 'pp.filter_genes'</option> |
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147 <option value="tl.filter_rank_genes_groups">Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories, using 'tl.filter_rank_genes_groups'</option> |
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148 <option value="pp.highly_variable_genes">Annotate (and filter) highly variable genes, using 'pp.highly_variable_genes'</option> |
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149 <option value="pp.subsample">Subsample to a fraction of the number of observations, using 'pp.subsample'</option> |
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150 <option value="pp.downsample_counts">Downsample counts from count matrix, using 'pp.downsample_counts'</option> |
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151 <option value="filter_marker">Filter markers from count matrix and marker list</option> |
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152 </param> |
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153 <when value="pp.filter_cells"> |
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154 <conditional name="filter"> |
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155 <param argument="filter" type="select" label="Filter"> |
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156 <option value="min_counts">Minimum number of counts</option> |
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157 <option value="max_counts">Maximum number of counts</option> |
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158 <option value="min_genes">Minimum number of genes expressed</option> |
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159 <option value="max_genes">Maximum number of genes expressed</option> |
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160 </param> |
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161 <when value="min_counts"> |
6ea5a05a260a
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162 <param argument="min_counts" type="integer" min="0" value="" label="Minimum number of counts required for a cell to pass filtering" help=""/> |
6ea5a05a260a
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163 </when> |
6ea5a05a260a
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iuc
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164 <when value="max_counts"> |
6ea5a05a260a
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165 <param argument="max_counts" type="integer" min="0" value="" label="Maximum number of counts required for a cell to pass filtering" help=""/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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166 </when> |
6ea5a05a260a
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iuc
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167 <when value="min_genes"> |
6ea5a05a260a
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168 <param argument="min_genes" type="integer" min="0" value="" label="Minimum number of genes expressed required for a cell to pass filtering" help=""/> |
6ea5a05a260a
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iuc
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169 </when> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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170 <when value="max_genes"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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171 <param argument="max_genes" type="integer" min="0" value="" label="Maximum number of genes expressed required for a cell to pass filtering" help=""/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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172 </when> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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173 </conditional> |
6ea5a05a260a
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174 </when> |
6ea5a05a260a
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iuc
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175 <when value="pp.filter_genes"> |
6ea5a05a260a
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176 <conditional name="filter"> |
6ea5a05a260a
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177 <param argument="filter" type="select" label="Filter"> |
6ea5a05a260a
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178 <option value="min_counts">Minimum number of counts</option> |
6ea5a05a260a
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179 <option value="max_counts">Maximum number of counts</option> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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180 <option value="min_cells">Minimum number of cells expressed</option> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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181 <option value="max_cells">Maximum number of cells expressed</option> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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182 </param> |
6ea5a05a260a
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183 <when value="min_counts"> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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184 <param argument="min_counts" type="integer" min="0" value="" label="Minimum number of counts required for a gene to pass filtering"/> |
0
6ea5a05a260a
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185 </when> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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186 <when value="max_counts"> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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187 <param argument="max_counts" type="integer" min="0" value="" label="Maximum number of counts required for a gene to pass filtering"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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188 </when> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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189 <when value="min_cells"> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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0
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190 <param argument="min_cells" type="integer" min="0" value="" label="Minimum number of cells expressed required for a gene to pass filtering"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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191 </when> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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192 <when value="max_cells"> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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193 <param argument="max_cells" type="integer" min="0" value="" label="Maximum number of cells expressed required for a gene to pass filtering"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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194 </when> |
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iuc
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195 </conditional> |
6ea5a05a260a
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196 </when> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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197 <when value="tl.filter_rank_genes_groups"> |
7
3c86f71498bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
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198 <param argument="key" type="text" optional="true" label="Key in adata.uns where the rank_genes_groups output is stored"> |
3c86f71498bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
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199 <expand macro="sanitize_query" /> |
3c86f71498bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
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200 </param> |
3c86f71498bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
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201 <param argument="groupby" type="text" optional="true" label="The key of the observations grouping to consider"> |
3c86f71498bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
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202 <expand macro="sanitize_query" /> |
3c86f71498bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
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203 </param> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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204 <expand macro="param_use_raw"/> |
7
3c86f71498bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
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205 <param argument="key_added" type="text" value="rank_genes_groups_filtered" label="Key that will contain new values"> |
3c86f71498bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
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206 <expand macro="sanitize_query" /> |
3c86f71498bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
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207 </param> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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208 <param argument="min_in_group_fraction" type="float" min="0" max="1" value="0.25" label="Minimum fraction of genes expressing the gene within the categories"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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209 <param argument="max_out_group_fraction" type="float" min="0" max="1" value="0.5" label="Maximum fraction of genes expressing the gene outside the categories"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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210 <param argument="min_fold_change" type="integer" value="2" label="Minimum fold change"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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211 </when> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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212 <when value="pp.highly_variable_genes"> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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213 <conditional name='flavor'> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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214 <param argument="flavor" type="select" label="Flavor for computing normalized dispersion"> |
3
0a6de5e65992
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
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215 <option value="seurat">Seurat</option> |
0a6de5e65992
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
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216 <option value="cell_ranger">Cell Ranger</option> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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217 </param> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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218 <when value="seurat"> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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219 <param argument="min_mean" type="float" value="0.0125" label="Minimal mean cutoff"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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220 <param argument="max_mean" type="float" value="3" label="Maximal mean cutoff"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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221 <param argument="min_disp" type="float" value="0.5" label="Minimal normalized dispersion cutoff"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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222 <param argument="max_disp" type="float" value="" optional="true" label="Maximal normalized dispersion cutoff"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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223 </when> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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224 <when value="cell_ranger"> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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225 <param argument="n_top_genes" type="integer" value="" label="Number of highly-variable genes to keep"/> |
0
6ea5a05a260a
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226 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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227 </conditional> |
6ea5a05a260a
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228 <param argument="n_bins" type="integer" value="20" label="Number of bins for binning the mean gene expression" help="Normalization is done with respect to each bin. If just a single gene falls into a bin, the normalized dispersion is artificially set to 1"/> |
3
0a6de5e65992
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
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229 <param argument="subset" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Inplace subset to highly-variable genes?" help="Otherwise it merely indicates highly variable genes."/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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230 </when> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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231 <when value="pp.subsample"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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232 <conditional name="type"> |
6ea5a05a260a
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iuc
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233 <param name="type" type="select" label="Type of subsampling"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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234 <option value="fraction">By fraction</option> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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235 <option value="n_obs">By number of observation</option> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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236 </param> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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237 <when value="fraction"> |
3
0a6de5e65992
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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238 <param argument="fraction" type="float" value="" label="Subsample to this 'fraction' of the number of observations"/> |
0
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239 </when> |
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240 <when value="n_obs"> |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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241 <param argument="n_obs" type="integer" min="0" value="" label="Subsample to this number of observations"/> |
0
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242 </when> |
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243 </conditional> |
1
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244 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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245 </when> |
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246 <when value="pp.downsample_counts"> |
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247 <param argument="counts_per_cell" type="integer" min="0" optional="true" label="Target total counts per cell" help="If a cell has more than ‘counts_per_cell’, it will be downsampled to this number. Resulting counts can be specified on a per cell basis by passing an array."/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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248 <param argument="total_counts" type="integer" min="0" optional="true" label="Target total counts" help="If the count matrix has more than total_counts it will be downsampled to have this number."/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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249 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling"/> |
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250 <param argument="replace" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sample the counts with replacement?"/> |
0
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251 </when> |
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252 <when value="filter_marker"> |
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253 <param argument="markerfile" type="data" format="tabular" label="List of markers" help="This should be a tsv where row = group (e.g. celltypes) and columns = markers."></param> |
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254 <param name="header" type="select" label="Header in the list of markers?"> |
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255 <option value="included">Header incldued</option> |
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256 <option value="not_included">Header not included</option> |
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257 </param> |
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258 <param argument="thresh_mean" type="float" min="0.0" value="1.0" label="Minimal average count of all cells of a group (e.g., celltype) for a particular marker" help="Increasing the threshold will result in a smaller marker set."/> |
aa0059118fb9
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259 <param argument="thresh_frac" type="float" min="0.0" max="1.0" value="0.1" label="Minimal fractions of cells that has a higher count than the average count of all cells of the group for the marker" help="Increasing this threshold might remove marker outliers."/> |
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260 <conditional name="layer_selection"> |
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261 <param name="use_raw" type="select" label="Use .X of adata to perform the filtering" help=""> |
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262 <option value="True">Yes</option> |
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263 <option value="False">No</option> |
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264 </param> |
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265 <when value="False"> |
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266 <param argument="layer" type="text" value="" label="Key from adata.layers whose value will be used to filter" help="If layers specified then use adata.layers[layer]."/> |
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267 </when> |
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268 <when value="True"/> |
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269 </conditional> |
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270 <param argument="groupby" type="text" value="" label="The key of the observation grouping to consider (e.g., celltype)" help=""> |
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271 <expand macro="sanitize_query" /> |
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272 </param> |
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273 </when> |
0
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274 </conditional> |
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275 <expand macro="inputs_common_advanced"/> |
0
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276 </inputs> |
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277 <outputs> |
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278 <expand macro="anndata_outputs"/> |
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279 <data name="marker_out" format="tabular" from_work_dir="marker.tsv" label="${tool.name} on ${on_string}: Markers"> |
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280 <filter>method['method'] == 'filter_marker'</filter> |
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281 </data> |
0
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282 </outputs> |
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283 <tests> |
11
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284 <test expect_num_outputs="2"> |
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285 <!-- test 1 --> |
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286 <param name="adata" value="krumsiek11.h5ad" /> |
0
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287 <conditional name="method"> |
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288 <param name="method" value="pp.filter_cells"/> |
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289 <conditional name="filter"> |
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290 <param name="filter" value="min_counts"/> |
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291 <param name="min_counts" value="3"/> |
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292 </conditional> |
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293 </conditional> |
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294 <assert_stdout> |
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295 <has_text_matching expression="336 × 11"/> |
0
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296 </assert_stdout> |
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297 <section name="advanced_common"> |
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298 <param name="show_log" value="true" /> |
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299 </section> |
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300 <output name="hidden_output"> |
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301 <assert_contents> |
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302 <has_text_matching expression="sc.pp.filter_cells"/> |
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303 <has_text_matching expression="min_counts=3"/> |
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304 </assert_contents> |
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305 </output> |
1
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306 <output name="anndata_out" file="pp.filter_cells.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/> |
0
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307 </test> |
11
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308 <test expect_num_outputs="2"> |
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309 <!-- test 2 --> |
1
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310 <param name="adata" value="krumsiek11.h5ad" /> |
0
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311 <conditional name="method"> |
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312 <param name="method" value="pp.filter_cells"/> |
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313 <conditional name="filter"> |
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314 <param name="filter" value="max_genes"/> |
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315 <param name="max_genes" value="100"/> |
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316 </conditional> |
6ea5a05a260a
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317 </conditional> |
6
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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318 <section name="advanced_common"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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319 <param name="show_log" value="true" /> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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320 </section> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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321 <output name="hidden_output"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
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322 <assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
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323 <has_text_matching expression="sc.pp.filter_cells"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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324 <has_text_matching expression="adata"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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325 <has_text_matching expression="max_genes=100"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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326 </assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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327 </output> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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328 <output name="anndata_out" file="pp.filter_cells.krumsiek11-max_genes.h5ad" ftype="h5ad" compare="sim_size"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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329 </test> |
11
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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330 <test expect_num_outputs="2"> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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331 <!-- test 3 --> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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332 <param name="adata" value="krumsiek11.h5ad" /> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff
changeset
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333 <conditional name="method"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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334 <param name="method" value="pp.filter_genes"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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335 <conditional name="filter"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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336 <param name="filter" value="min_counts"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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337 <param name="min_counts" value="3"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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338 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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339 </conditional> |
6
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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340 <section name="advanced_common"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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341 <param name="show_log" value="true" /> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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342 </section> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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343 <output name="hidden_output"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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344 <assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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345 <has_text_matching expression="sc.pp.filter_genes"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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346 <has_text_matching expression="min_counts=3"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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347 </assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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348 </output> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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349 <output name="anndata_out" file="pp.filter_genes.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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350 </test> |
11
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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351 |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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352 <!-- test 4 --> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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353 <!-- Fails to write to anndata after tl.filter_rank_genes_groups |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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354 Issue has been reported here: https://github.com/scverse/anndata/issues/726 |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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355 The current fix is: del adata.uns['rank_genes_groups_filtered'] --> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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356 <!--<test expect_num_outputs="2"> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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357 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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358 <conditional name="method"> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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359 <param name="method" value="tl.filter_rank_genes_groups"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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360 <param name="key" value="rank_genes_groups"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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361 <param name="use_raw" value="False"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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362 <param name="key_added" value="rank_genes_groups_filtered"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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363 <param name="min_in_group_fraction" value="0.25"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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364 <param name="max_out_group_fraction" value="0.5"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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365 <param name="min_fold_change" value="3"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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366 </conditional> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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367 <section name="advanced_common"> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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368 <param name="show_log" value="true" /> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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369 </section> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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370 <output name="hidden_output"> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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371 <assert_contents> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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372 <has_text_matching expression="tl.filter_rank_genes_groups"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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373 <has_text_matching expression="key='rank_genes_groups'"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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374 <has_text_matching expression="use_raw=False"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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375 <has_text_matching expression="log=False"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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376 <has_text_matching expression="key_added='rank_genes_groups_filtered'"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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377 <has_text_matching expression="min_in_group_fraction=0.25"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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378 <has_text_matching expression="max_out_group_fraction=0.5"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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379 <has_text_matching expression="min_fold_change=3"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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380 </assert_contents> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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381 </output> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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382 <output name="anndata_out" file="pp.filter_rank_genes_groups.h5ad" ftype="h5ad" compare="sim_size"/> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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383 </test>--> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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384 <test expect_num_outputs="2"> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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385 <!-- test 5 --> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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386 <param name="adata" value="blobs.h5ad"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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387 <conditional name="method"> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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388 <param name="method" value="pp.highly_variable_genes"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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389 <conditional name="flavor"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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390 <param name="flavor" value="seurat"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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391 <param name="min_mean" value="0.0125"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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392 <param name="max_mean" value="3"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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393 <param name="min_disp" value="0.5"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
394 </conditional> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
395 <param name="n_bins" value="20"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
396 <param name="subset" value="false"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
397 </conditional> |
6
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
398 <section name="advanced_common"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
399 <param name="show_log" value="true" /> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
400 </section> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
401 <output name="hidden_output"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
402 <assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
403 <has_text_matching expression="sc.pp.highly_variable_genes"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
404 <has_text_matching expression="flavor='seurat'"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
405 <has_text_matching expression="min_mean=0.0125"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
406 <has_text_matching expression="max_mean=3"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
407 <has_text_matching expression="min_disp=0.5"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
408 <has_text_matching expression="n_bins=20"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
409 <has_text_matching expression="subset=False"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
410 </assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
411 </output> |
8
f87ed6503715
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
iuc
parents:
7
diff
changeset
|
412 <output name="anndata_out" file="pp.highly_variable_genes.seurat.blobs.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.2"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
413 </test> |
11
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents:
10
diff
changeset
|
414 <test expect_num_outputs="2"> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents:
10
diff
changeset
|
415 <!-- test 6 --> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
416 <param name="adata" value="krumsiek11.h5ad" /> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
417 <conditional name="method"> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
418 <param name="method" value="pp.highly_variable_genes"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
419 <conditional name="flavor"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
420 <param name="flavor" value="cell_ranger"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
421 <param name="n_top_genes" value="2"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
422 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
423 <param name="n_bins" value="20"/> |
3
0a6de5e65992
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
2
diff
changeset
|
424 <param name="subset" value="true"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
425 </conditional> |
6
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
426 <section name="advanced_common"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
427 <param name="show_log" value="true" /> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
428 </section> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
429 <output name="hidden_output"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
430 <assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
431 <has_text_matching expression="sc.pp.highly_variable_genes"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
432 <has_text_matching expression="flavor='cell_ranger'"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
433 <has_text_matching expression="n_top_genes=2"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
434 <has_text_matching expression="n_bins=20"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
435 <has_text_matching expression="subset=True"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
436 </assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
437 </output> |
8
f87ed6503715
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
iuc
parents:
7
diff
changeset
|
438 <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.9"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
439 </test> |
11
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents:
10
diff
changeset
|
440 <test expect_num_outputs="2"> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents:
10
diff
changeset
|
441 <!-- test 7 --> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
442 <param name="adata" value="krumsiek11.h5ad" /> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
443 <conditional name="method"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
444 <param name="method" value="pp.subsample"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
445 <conditional name="type"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
446 <param name="type" value="fraction" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
447 <param name="fraction" value="0.5"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
448 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
449 <param name="random_state" value="0"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
450 </conditional> |
6
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
451 <section name="advanced_common"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
452 <param name="show_log" value="true" /> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
453 </section> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
454 <output name="hidden_output"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
455 <assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
456 <has_text_matching expression="sc.pp.subsample"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
457 <has_text_matching expression="fraction=0.5"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
458 <has_text_matching expression="random_state=0"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
459 </assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
460 </output> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
461 <output name="anndata_out" file="pp.subsample.krumsiek11_fraction.h5ad" ftype="h5ad" compare="sim_size"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
462 </test> |
11
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents:
10
diff
changeset
|
463 <test expect_num_outputs="2"> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents:
10
diff
changeset
|
464 <!-- test 8 --> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
465 <param name="adata" value="krumsiek11.h5ad" /> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
466 <conditional name="method"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
467 <param name="method" value="pp.subsample"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
468 <conditional name="type"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
469 <param name="type" value="n_obs" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
470 <param name="n_obs" value="10"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
471 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
472 <param name="random_state" value="0"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
473 </conditional> |
6
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
474 <section name="advanced_common"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
475 <param name="show_log" value="true" /> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
476 </section> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
477 <output name="hidden_output"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
478 <assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
479 <has_text_matching expression="sc.pp.subsample"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
480 <has_text_matching expression="n_obs=10"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
481 <has_text_matching expression="random_state=0"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
482 </assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
483 </output> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
484 <output name="anndata_out" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5ad" compare="sim_size"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
485 </test> |
11
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents:
10
diff
changeset
|
486 <test expect_num_outputs="2"> |
2d02d9702d3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents:
10
diff
changeset
|
487 <!-- test 9 --> |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
488 <param name="adata" value="random-randint.h5ad" /> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
489 <conditional name="method"> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
490 <param name="method" value="pp.downsample_counts"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
491 <param name="total_counts" value="20000"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
492 <param name="random_state" value="0"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
493 <param name="replace" value="false"/> |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
494 </conditional> |
6
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
495 <section name="advanced_common"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
496 <param name="show_log" value="true" /> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
497 </section> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
498 <output name="hidden_output"> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
499 <assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
500 <has_text_matching expression="sc.pp.downsample_counts"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
501 <has_text_matching expression="total_counts=20000"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
502 <has_text_matching expression="random_state=0"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
503 <has_text_matching expression="replace=False"/> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
504 </assert_contents> |
a97abb8cd15b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
505 </output> |
8
f87ed6503715
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
iuc
parents:
7
diff
changeset
|
506 <output name="anndata_out" file="pp.downsample_counts.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="10000000" delta_frac="0.5"/> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
507 </test> |
15
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
508 <test expect_num_outputs="3"> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
509 <!-- test 10 --> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
510 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" /> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
511 <conditional name="method"> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
512 <param name="method" value="filter_marker"/> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
513 <param name="markerfile" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv"/> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
514 <param name="thresh_mean" value="1.0"/> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
515 <param name="thresh_frac" value="0.2"/> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
516 <param name="layer_selection" value="True"/> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
517 <param name="groupby" value="bulk_labels"/> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
518 </conditional> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
519 <section name="advanced_common"> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
520 <param name="show_log" value="true" /> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
521 </section> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
522 <output name="hidden_output"> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
523 <assert_contents> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
524 <has_text_matching expression="adata, key, x, 1.0, 0.2, 'bulk_labels'"/> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
525 </assert_contents> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
526 </output> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
527 <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" ftype="h5ad"> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
528 <assert_contents> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
529 <has_h5_keys keys="obs, var, uns" /> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
530 </assert_contents> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
531 </output> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
532 <output name="marker_out" file="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv" ftype="tabular" compare="sim_size"/> |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
533 </test> |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
534 </tests> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
535 <help><![CDATA[ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
536 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
537 Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
538 ======================================================================================== |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
539 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
540 For instance, only keep cells with at least `min_counts` counts or |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
541 `min_genes` genes expressed. This is to filter measurement outliers, i.e., |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
542 "unreliable" observations. |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
543 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
544 Only provide one of the optional parameters `min_counts`, `min_genes`, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
545 `max_counts`, `max_genes` per call. |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
546 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
547 More details on the `scanpy documentation |
14
d636ce5cde16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents:
12
diff
changeset
|
548 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_cells.html>`__ |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
549 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
550 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
551 Filter genes based on number of cells or counts (`pp.filter_genes`) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
552 =================================================================== |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
553 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
554 Keep genes that have at least `min_counts` counts or are expressed in at |
6ea5a05a260a
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555 least `min_cells` cells or have at most `max_counts` counts or are expressed |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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556 in at most `max_cells` cells. |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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557 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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558 Only provide one of the optional parameters `min_counts`, `min_cells`, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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559 `max_counts`, `max_cells` per call. |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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560 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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561 More details on the `scanpy documentation |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
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562 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_genes.html>`__ |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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563 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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564 |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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565 Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (`tl.filter_rank_genes_groups`) |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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566 ========================================================================================================================================================== |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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567 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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568 More details on the `scanpy documentation |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
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569 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__ |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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570 |
0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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571 |
1
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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572 Annotate highly variable genes (`pp.highly_variable_genes`) |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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573 =========================================================== |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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574 |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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575 It expects logarithmized data. |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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576 |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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577 Depending on flavor, this reproduces the R-implementations of Seurat or Cell Ranger. The normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for genes falling into a given bin for mean expression of genes. This means that for each bin of mean expression, highly variable genes are selected. |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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578 |
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579 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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580 Subsample to a fraction of the number of observations (`pp.subsample`) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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581 ====================================================================== |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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582 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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583 More details on the `scanpy documentation |
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584 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.subsample.html>`__ |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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585 |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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586 Downsample counts (`pp.downsample_counts`) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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587 ========================================== |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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588 |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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589 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This |
6a76b60e05f5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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590 has been implemented by M. D. Luecken. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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591 |
15
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592 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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593 Filter marker genes (`filter_marker`) |
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594 ====================================================================== |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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595 |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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596 This option is specific for celltype marker gene detection. You can generate a celltype marker gene file (tsv) with **COSG** provided at Galaxy. |
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597 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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598 The marker gene file should have as rows celltypes and columns as marker genes. Each celltype can have varying number of marker genes. |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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599 |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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600 A marker gene is returned (retained in the list) if the mean expression of the marker gene is bigger than the threshold of mean expression (thresh_mean) and if the fraction of cells with the marker gene expression is equal or higher than the cell fraction threshold (thresh_frac). |
aa0059118fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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601 |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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602 More details on the `scanpy documentation |
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603 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.downsample_counts.html>`__ |
0
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604 |
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605 |
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606 ]]></help> |
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607 <expand macro="citations"/> |
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608 </tool> |