comparison scanpy-run-umap.xml @ 15:135e8cacb57e draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"

14:62c31dc2e5d5

<?xml version="1.0" encoding="utf-8"?>
<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>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-run-umap
    --neighbors-key '${use_graph}'
    --key-added '${key_added}'
#if $embeddings
    --export-embedding embeddings.tsv
#end if
#if $settings.default == "false"
    --n-components ${settings.n_components}

        --maxiter ${settings.maxiter}
    #end if
#end if
    @INPUT_OPTS@
    @OUTPUT_OPTS@

]]></command>

  <inputs>
    <expand macro="input_object_params"/>

15:135e8cacb57e

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
  <description>visualise cell clusters using UMAP</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-run-umap
#set neighbors_key = $use_graph.replace('INPUT_OBJ', $input_obj_file.__getattr__('name'))
#set embeddings_tsv='embeddings.tsv'
--neighbors-key '${neighbors_key}'
#if $key_added
    #if $neighbors_key
        #set key_added = $key_added.replace('NEIGHBORS_KEY', $neighbors_key.__str__)
    #set embeddings_tsv="embeddings_" + $key_added.__str__ + ".tsv"    
#end if
    --key-added '${key_added}'
#end if
#if $embeddings
    --export-embedding embeddings.tsv
#end if
#if $settings.default == "false"
    --n-components ${settings.n_components}

        --maxiter ${settings.maxiter}
    #end if
#end if
    @INPUT_OPTS@
    @OUTPUT_OPTS@
#if $embeddings
    #if $embeddings_tsv != 'embeddings.tsv'
        && mv '${embeddings_tsv}' embeddings.tsv
    #end if
#end if

]]></command>

  <inputs>
    <expand macro="input_object_params"/>