| Previous changeset 11:10893b1647ff (2020-06-05) Next changeset 13:fb50577dc31d (2020-09-10) |
|
Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty" |
|
modified:
scanpy-run-umap.xml scanpy_macros2.xml |
| b |
| diff -r 10893b1647ff -r f53bb2c1fa07 scanpy-run-umap.xml --- a/scanpy-run-umap.xml Fri Jun 05 09:14:06 2020 -0400 +++ b/scanpy-run-umap.xml Mon Sep 07 14:00:37 2020 +0000 |
| [ |
| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> +<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>visualise cell clusters using UMAP</description> <macros> <import>scanpy_macros2.xml</import> @@ -8,10 +8,10 @@ <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-run-umap - --use-graph '${use_graph}' + --neighbors-key '${use_graph}' --key-added '${key_added}' #if $embeddings - --export-embedding embeddings.csv + --export-embedding embeddings.tsv #end if #if $settings.default == "false" --n-components ${settings.n_components} @@ -36,8 +36,8 @@ <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> - <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/> - <param name="use_graph" argument="--use-graph" value="neighbors" type="text" + <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/> + <param name="use_graph" argument="--neighbors-key" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/> <param name="key_added" argument="--key-added" type="text" optional="true" label="Additional suffix to the name of the slot to save the embedding"/> @@ -65,7 +65,7 @@ <outputs> <expand macro="output_data_obj" description="UMAP object"/> - <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: UMAP embeddings"> + <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: UMAP embeddings"> <filter>embeddings</filter> </data> </outputs> @@ -79,9 +79,9 @@ <param name="embeddings" value="true"/> <param name="random_seed" value="0"/> <output name="output_h5" file="run_umap.h5" ftype="h5" compare="sim_size"/> - <output name="output_embed" file="run_umap.embeddings.csv" ftype="csv" compare="sim_size"> + <output name="output_embed" file="run_umap.embeddings.tsv" ftype="tabular" compare="sim_size"> <assert_contents> - <has_n_columns n="2" sep=","/> + <has_n_columns n="3"/> </assert_contents> </output> </test> |
| b |
| diff -r 10893b1647ff -r f53bb2c1fa07 scanpy_macros2.xml --- a/scanpy_macros2.xml Fri Jun 05 09:14:06 2020 -0400 +++ b/scanpy_macros2.xml Mon Sep 07 14:00:37 2020 +0000 |
| [ |
| @@ -1,10 +1,13 @@ <macros> - <token name="@TOOL_VERSION@">1.4.3</token> + <token name="@TOOL_VERSION@">1.6.0</token> <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> <token name="@PROFILE@">18.01</token> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ + 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca. 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes. @@ -46,7 +49,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.10">scanpy-scripts</requirement> + <requirement type="package" version="0.3.0">scanpy-scripts</requirement> <yield/> </requirements> </xml> |