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comparison scanpy_macros2.xml @ 2:ba18139e7400 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
author ebi-gxa
date Mon, 25 Nov 2019 14:37:55 -0500
parents 339d205356c6
children d586ebb8ff43
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1:339d205356c6 2:ba18139e7400
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.4.3</token> 2 <token name="@TOOL_VERSION@">1.4.3</token>
3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> 3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
4 <token name="@VERSION_HISTORY@"><![CDATA[ 4 <token name="@VERSION_HISTORY@"><![CDATA[
5 **Version history** 5 **Version history**
6
7 1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.
6 8
7 1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3). 9 1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).
8 10
9 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2). 11 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
10 12
15 ]]></token> 17 ]]></token>
16 <token name="@INPUT_OPTS@"> 18 <token name="@INPUT_OPTS@">
17 --input-format '${input_format}' input.h5 19 --input-format '${input_format}' input.h5
18 </token> 20 </token>
19 <token name="@OUTPUT_OPTS@"> 21 <token name="@OUTPUT_OPTS@">
20 --show-obj stdout --output-format '${output_format}' output.h5 22 #if str($output_format).startswith('anndata')
23 --show-obj stdout --output-format anndata output.h5
24 #else
25 --show-obj stdout --output-format loom output.h5
26 #end if
21 </token> 27 </token>
22 <token name="@PLOT_OPTS@"> 28 <token name="@PLOT_OPTS@">
23 #if $fig_title 29 #if $fig_title
24 --title '${fig_title}' 30 --title '${fig_title}'
25 #end if 31 #end if
31 </token> 37 </token>
32 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token> 38 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
33 39
34 <xml name="requirements"> 40 <xml name="requirements">
35 <requirements> 41 <requirements>
36 <requirement type="package" version="0.2.6">scanpy-scripts</requirement> 42 <requirement type="package" version="0.2.8">scanpy-scripts</requirement>
37 <yield/> 43 <yield/>
38 </requirements> 44 </requirements>
39 </xml> 45 </xml>
40 46
41 <xml name="citations"> 47 <xml name="citations">
53 }</citation> 59 }</citation>
54 </citations> 60 </citations>
55 </xml> 61 </xml>
56 62
57 <xml name="input_object_params"> 63 <xml name="input_object_params">
58 <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 format"/> 64 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData/Loom format"/>
59 <param name="input_format" argument="--input-format" type="select" label="Format of input object"> 65 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
60 <option value="anndata" selected="true">AnnData format hdf5</option> 66 <option value="anndata" selected="true">AnnData format hdf5</option>
61 <option value="loom">Loom format hdf5</option> 67 <option value="loom">Loom format hdf5</option>
62 </param> 68 </param>
63 </xml> 69 </xml>
64 70
65 <xml name="output_object_params"> 71 <xml name="output_object_params">
66 <param name="output_format" argument="--output-format" type="select" label="Format of output object"> 72 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
67 <option value="anndata" selected="true">AnnData format hdf5</option> 73 <option value="anndata_h5ad" selected="true">AnnData format</option>
68 <option value="loom">Loom format hdf5</option> 74 <option value="anndata">AnnData format (h5 for older versions)</option>
75 <option value="loom">Loom format</option>
76 <option value="loom_legacy">Loom format (h5 for older versions)</option>
69 </param> 77 </param>
78 </xml>
79
80 <xml name="output_object_params_no_loom">
81 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
82 <option value="anndata_h5ad" selected="true">AnnData format</option>
83 <option value="anndata">AnnData format (h5 for older versions)</option>
84 </param>
85 </xml>
86
87 <xml name="output_data_obj_no_loom" token_description="operation">
88 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
89 <filter>output_format == 'anndata_h5ad'</filter>
90 </data>
91 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
92 <filter>output_format == 'anndata'</filter>
93 </data>
94 </xml>
95
96 <xml name="output_data_obj" token_description="operation">
97 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
98 <filter>output_format == 'anndata_h5ad'</filter>
99 </data>
100 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
101 <filter>output_format == 'anndata'</filter>
102 </data>
103 <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
104 <filter>output_format == 'loom_legacy'</filter>
105 </data>
106 <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
107 <filter>output_format == 'loom'</filter>
108 </data>
70 </xml> 109 </xml>
71 110
72 <xml name="output_plot_params"> 111 <xml name="output_plot_params">
73 <param name="fig_title" argument="--title" type="text" label="Figure title"/> 112 <param name="fig_title" argument="--title" type="text" label="Figure title"/>
74 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/> 113 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>