| Previous changeset 14:fb9bd74c32b0 (2020-09-11) Next changeset 16:1670af5eee46 (2020-10-07) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty" |
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modified:
scanpy-find-markers.xml |
| b |
| diff -r fb9bd74c32b0 -r cc776860fae1 scanpy-find-markers.xml --- a/scanpy-find-markers.xml Fri Sep 11 11:05:29 2020 +0000 +++ b/scanpy-find-markers.xml Wed Sep 30 11:16:08 2020 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>to find differentially expressed genes between groups</description> <macros> <import>scanpy_macros2.xml</import> @@ -9,10 +9,15 @@ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-find-markers #if $output_markers - --save output.csv + --save diffexp.tsv #end if --n-genes '${n_genes}' +#set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name')) --groupby '${groupby}' +#if $settings.key_added + #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__) + --key-added '${key_added}' +#end if #if $settings.default == "false" --method '${settings.method}' ${settings.use_raw} @@ -31,13 +36,15 @@ <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> - <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/> + <param name="output_markers" type="boolean" checked="true" label="Output markers table in tsv format"/> <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/> <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/> <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> + <param name="key_added" argument="--key-added" type="text" optional="true" + label="The key in adata.uns information is saved to. If included, the keyword 'GROUPBY' will be substituted with the value of the groupby setting."/> <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes"> <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option> <option value="t-test">t-test</option> @@ -64,24 +71,26 @@ <outputs> <expand macro="output_data_obj" description="Marker genes"/> - <data name="output_csv" format="csv" from_work_dir="output.csv" label="${tool.name} on ${on_string}: Marker table"> + <data name="output_tsv" format="tabular" from_work_dir="diffexp.tsv" label="${tool.name} on ${on_string}: Marker table"> <filter>output_markers</filter> </data> </outputs> <tests> <test> - <param name="input_obj_file" value="find_cluster.h5"/> + <param name="input_obj_file" value="louvain_1.0"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> - <param name="output_csv" value="true"/> + <param name="output_tsv" value="true"/> <param name="n_genes" value="50"/> - <param name="output_markers" value="false"/> + <param name="output_markers" value="true"/> <param name="default" value="false"/> - <param name="groupby" value="louvain"/> + <param name="groupby" value="INPUT_OBJ"/> + <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> |