Mercurial > repos > ebi-gxa > scanpy_find_markers
diff scanpy-find-markers.xml @ 17:f04dd4e5b6a7 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
| author | ebi-gxa |
|---|---|
| date | Thu, 15 Oct 2020 16:06:41 +0000 |
| parents | 1670af5eee46 |
| children | bfdca1eb4548 |
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--- a/scanpy-find-markers.xml Wed Oct 07 16:06:38 2020 +0000 +++ b/scanpy-find-markers.xml Thu Oct 15 16:06:41 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> +<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> <description>to find differentially expressed genes between groups</description> <macros> <import>scanpy_macros2.xml</import> @@ -12,7 +12,13 @@ --save diffexp.tsv #end if --n-genes '${n_genes}' -#set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name')) +#if $groupby_file + #set f = open($groupby_file.__str__) + #set groupby = f.read().strip() + #silent f.close +#else + #set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name')) +#end if --groupby '${groupby}' #if $settings.default == "false" #if $settings.key_added @@ -39,6 +45,8 @@ <param name="output_markers" type="boolean" checked="true" label="Output markers table in tsv format"/> <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/> <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/> + <param name="groupby_file" argument="--groupby" type="data" format="txt,tsv" optional="true" + label="File with groupby. Overrides the groupby setting"/> <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> @@ -92,6 +100,21 @@ <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/> <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> </test> + <test> + <param name="input_obj_file" value="louvain_1.0"/> + <param name="input_format" value="anndata"/> + <param name="output_format" value="anndata"/> + <param name="output_tsv" value="true"/> + <param name="n_genes" value="50"/> + <param name="output_markers" value="true"/> + <param name="default" value="false"/> + <param name="groupby_file" value="groupby.txt"/> + <param name="key_added" value="GROUPBY_marker"/> + <param name="method" value="t-test_overestim_var"/> + <param name="rankby_abs" value="false"/> + <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/> + <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> + </test> </tests> <help><![CDATA[