| Previous changeset 10:4722394f6af9 (2020-06-05) Next changeset 12:260c8932c0b7 (2020-09-10) |
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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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty" |
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modified:
scanpy-run-fdg.xml scanpy_macros2.xml |
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| diff -r 4722394f6af9 -r dd27b39c5c12 scanpy-run-fdg.xml --- a/scanpy-run-fdg.xml Fri Jun 05 09:01:17 2020 -0400 +++ b/scanpy-run-fdg.xml Mon Sep 07 13:09:43 2020 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> +<tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>visualise cell clusters using force-directed graph</description> <macros> <import>scanpy_macros2.xml</import> @@ -8,17 +8,25 @@ <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-cli embed fdg - --use-graph '${use_graph}' - --key-added '${key_added}' + --key-added-ext '${key_added_ext}' #if $embeddings - --export-embedding embeddings.csv + --export-embedding embeddings.tsv #end if #if $settings.default == "false" + #if $settings.neighbors_key + --neighbors-key '${settings.neighbors_key}' + #end if + #if $settings.obsp + --obsp '${settings.obsp}' + #end if --random-state ${settings.random_seed} --layout ${settings.layout} #if $settings.init_pos --init-pos '${settings.init_pos}' #end if + #if $settings.root + --root '${settings.root}' + #end if #end if @INPUT_OPTS@ @OUTPUT_OPTS@ @@ -28,24 +36,31 @@ <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" - label="Name of the slot that holds the KNN graph"/> - <param name="key_added" argument="--key-added" type="text" optional="true" + <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/> + <param name="key_added_ext" argument="--key-added-ext" type="text" optional="true" label="Additional suffix to the name of the slot to save the embedding"/> <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> + <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text" + label="Name of the slot that holds the KNN graph"/> + <param name="obsp" type="boolean" checked="false" label="Use .obsp[obsp] as adjacency" help="You can’t specify both obsp and neighbors-key at the same time."/> <param name="init_pos" argument="--init-pos" type="text" label="Method to initialise embedding, any key for adata.obsm or choose from the preset methods"> <option value="paga">paga</option> </param> <param name="layout" argument="--layout" type="select" label="Graph layout"> - <option value="fa" selected="true">fa</option> - <option value="fr">fr</option> + <option value="fa">fa</option> + <option value="fr" selected="true">fr</option> <option value="grid_fr">grid fr</option> + <option value="kk">kk</option> + <option value="lgl">lgl</option> + <option value="drl">drl</option> + <option value="rt">rt</option> + <option value="rt_circular">rt_circular</option> </param> + <param name="root" argument="--root" type="integer" optional="true" label="Root for tree layouts"/> <param name="random_seed" argument="--random-state" type="integer" value="0" label="Seed for numpy random number generator"/> </when> </conditional> @@ -53,7 +68,7 @@ <outputs> <expand macro="output_data_obj" description="FDG object"/> - <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: FDG embeddings"> + <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: FDG embeddings"> <filter>embeddings</filter> </data> </outputs> @@ -67,9 +82,9 @@ <param name="embeddings" value="true"/> <param name="random_seed" value="0"/> <output name="output_h5" file="run_fdg.h5" ftype="h5" compare="sim_size"/> - <output name="output_embed" file="run_fdg.embeddings.csv" ftype="csv" compare="sim_size"> + <output name="output_embed" file="run_fdg.embeddings.tsv" ftype="tabular" compare="sim_size"> <assert_contents> - <has_n_columns n="2" sep=","/> + <has_n_columns n="3"/> </assert_contents> </output> </test> |
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| diff -r 4722394f6af9 -r dd27b39c5c12 scanpy_macros2.xml --- a/scanpy_macros2.xml Fri Jun 05 09:01:17 2020 -0400 +++ b/scanpy_macros2.xml Mon Sep 07 13:09:43 2020 +0000 |
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| @@ -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> |