annotate sccaf_macros.xml @ 0:ca26d4b4b02c draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
author ebi-gxa
date Mon, 14 Oct 2019 08:11:29 -0400
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children 647d34f125bc
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ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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1 <macros>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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2 <xml name="requirements">
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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3 <requirements>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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4 <requirement type="package" version="@TOOL_VERSION@">sccaf</requirement>
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5 </requirements>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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6 </xml>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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7 <token name="@TOOL_VERSION@">0.0.7</token>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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8 <token name="@SCCAF_INTRO@">
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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9 SCCAF explained
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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10 ===============
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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11
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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12 Single Cell Clustering Assessment Framework (SCCAF) is a novel method for
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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13 automated identification of putative cell types from single cell RNA-seq
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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14 (scRNA-seq) data. By iteratively applying clustering and a machine learning
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15 approach to gene expression profiles of a given set of cells, SCCAF
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16 simultaneously identifies distinct cell groups and a weighted list of feature
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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17 genes for each group. The feature genes, which are overexpressed in the
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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18 particular cell group, jointly discriminate the given cell group from other
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19 cells. Each such group of cells corresponds to a putative cell type or state,
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20 characterised by the feature genes as markers.
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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21 </token>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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22 <token name="@HELP@">More information can be found at https://github.com/SCCAF/SCCAF</token>
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23 <token name="@PLOT_OPTS@">
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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24 #if $do_plotting.plot
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25 -P output.png
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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26 --projectio $do_plotting.projection
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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27 --components $do_plotting.components
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28 #if $do_plotting.color_by
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29 --color-by $do_plotting.color_by
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30 #end if
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31 #if $do_plotting.groups
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32 --group $do_plotting.groups
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33 #end if
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34 #if $do_plotting.use_raw
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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35 --use-raw
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36 #end if
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37 #if $do_plotting.palette
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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38 --palette $do_plotting.palette
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39 #end if
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40 #if $do_plotting.show_edges
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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41 --edges
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42 #end if
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43 #if $do_plotting.show_arrows
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44 --arrows
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45 #end if
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46 #if not $do_plotting.color_order
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47 --no-sort-order
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48 #end if
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49 #if $do_plotting.omit_frame
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50 --frameoff
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51 #end if
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52 #end if
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53 </token>
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54 <xml name="citations">
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55 <citations>
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56 <citation type="doi"></citation>
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57 <citation type="bibtex">
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58 @misc{githubsccaf,
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59 author = {Miao, Zhichao},
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60 year = {2018},
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61 title = {SCCAF},
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62 publisher = {GitHub},
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63 journal = {GitHub repository},
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64 url = {https://github.com/Functional-Genomics/SCCAF},
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65 }</citation>
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66 <yield />
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67 </citations>
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68 </xml>
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69 <xml name="input_object_params">
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70 <param name="input_obj_file" argument="--input-object-file" type="data" format="h5" label="Input object in AnnData hdf5 format" help="Normally the result of Scanpy (or equivalent), which already has both a visualisation (either tSNE, UMAP or PCA - needed) and clustering (ideally) pre-computed."/>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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71 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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72 <option value="anndata" selected="true">AnnData format hdf5</option>
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73 <option value="loom">Loom format hdf5, current support is incomplete</option>
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74 </param>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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75 </xml>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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76 <xml name="output_object_params">
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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77 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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78 <option value="anndata" selected="true">AnnData format hdf5</option>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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79 <option value="loom">Loom format hdf5, current support is defective</option>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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80 </param>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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81 </xml>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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82 <xml name="output_plot_params">
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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83 <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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84 <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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85 <param name="projection" argument="--projection" type="select" label="Plot projection">
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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86 <option value="2d" selected="true">2D</option>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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87 <option value="3d">3D</option>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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88 </param>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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89 <param name="components" argument="--components" type="text" value="1,2" label="Components to plot, comma separated integers"/>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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90 <param name="palette" argument="--palette" type="text" optional="true" label="Palette"/>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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91 <param name="use_raw" argument="--use-raw" type="boolean" checked="false" label="Use raw attributes if present"/>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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92 <param name="show_edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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93 <param name="show_arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
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94 <param name="color_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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95 <param name="omit_frame" argument="--frameoff" type="boolean" checked="false" label="Show frame"/>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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96 </xml>
ca26d4b4b02c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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97 </macros>