comparison scanpy-run-fdg.xml @ 16:a6190ae4fe16 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 045c1232e9d8cdc7bc084e089900e9bd17fc47e1-dirty"

15:5d2c8acd2ae4

<?xml version="1.0" encoding="utf-8"?>
<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>
  </macros>
  <expand macro="requirements"/>

      <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">fa</option>
          <option value="fr" selected="true">fr</option>
          <option value="grid_fr">grid fr</option>
          <option value="kk">kk</option>

16:a6190ae4fe16

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
  <description>visualise cell clusters using force-directed graph</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

      <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"/>
        <param name="layout" argument="--layout" type="select" label="Graph layout">
          <option value="fa">fa</option>
          <option value="fr" selected="true">fr</option>
          <option value="grid_fr">grid fr</option>
          <option value="kk">kk</option>