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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 e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty" |
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modified:
scanpy-run-tsne.xml |
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| diff -r c4a20a57d825 -r b5e1939cc155 scanpy-run-tsne.xml --- a/scanpy-run-tsne.xml Fri Sep 11 11:05:07 2020 +0000 +++ b/scanpy-run-tsne.xml Thu Sep 17 16:28:31 2020 +0000 |
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| @@ -1,27 +1,37 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>visualise cell clusters using tSNE</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ +#from pathlib import Path +#set embeddings_tsv='embeddings.tsv' ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-run-tsne #if $use_rep != "auto" --use-rep '${use_rep}' #end if -#if $key_added - --key-added '${key_added}' -#end if #if $embeddings --export-embedding embeddings.tsv #end if #if $settings.default == "false" #if $settings.perplexity_file - --perplexity \$( cat $settings.perplexity_file ) - #else - --perplexity '${settings.perplexity}' + #set perplexity = Path($settings.perplexity_file.__str__).read_text().strip() + #elif $settings.perplexity + #set perplexity = $settings.perplexity.__str__.strip() + #end if + #if $perplexity + --perplexity '$perplexity' + #end if + #if $settings.key_added + #set key_added = $settings.key_added + #if $perplexity + #set key_added = $key_added.replace('PERPLEXITY', $perplexity.__str__) + #end if + --key-added '${key_added}' + #set embeddings_tsv="embeddings_" + $key_added.__str__ + ".tsv" #end if --early-exaggeration '${settings.early_exaggeration}' --learning-rate '${settings.learning_rate}' @@ -40,6 +50,11 @@ #end if @INPUT_OPTS@ @OUTPUT_OPTS@ +#if $embeddings + #if $embeddings_tsv != 'embeddings.tsv' + && mv '${embeddings_tsv}' embeddings.tsv + #end if +#end if ]]></command> @@ -53,13 +68,12 @@ <option value="X">X, use normalised expression values</option> <option value="auto" selected="true">Automatically chosen based on problem size</option> </param> - <param name="key_added" argument="--key-added" 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="key_added" argument="--key-added" type="text" optional="true" + label="Additional suffix to the name of the slot to save the embedding" help="If included, PERPLEXITY will be substituted with the value of the perplexity setting."/> <param name="perplexity" argument="--perplexity" type="float" value="30" label="The perplexity is related to the number of nearest neighbours, select a value between 5 and 50"/> <param name="perplexity_file" argument="--perplexity" type="data" format="txt,tsv" label="The perplexity is related to the number of nearest neighbours" help="For use with the parameter iterator. Overrides the persplexity option above" optional="true"/> <param name="early_exaggeration" argument="--early-exaggeration" type="float" value="12" label="Controls the tightness within and between clusters"/> |