Mercurial > repos > ebi-gxa > scanpy_integrate_harmony

comparison scanpy_macros2.xml @ 12:3111bcf039dd 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 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
author ebi-gxa
date Thu, 16 Feb 2023 13:29:06 +0000
parents ca0c7251e415
children 18e01a7c55c6
comparison
equal deleted inserted replaced
11:ca0c7251e415 12:3111bcf039dd
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.8.1+3</token> 2 <token name="@TOOL_VERSION@">1.8.1</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="@PROFILE@">18.01</token> 4 <token name="@PROFILE@">18.01</token>
5 <token name="@VERSION_HISTORY@"><![CDATA[ 5 <token name="@VERSION_HISTORY@"><![CDATA[
6 **Version history** 6 **Version history**
7 1.8.1+galaxy9: Fixes version label to get versions sorted properly on Galaxy (equivalent to 1.8.1+3+galaxy0). In addition, adds ability to make fields unique in AnnData operations,
8 adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required.
7 9
8 1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper. 10 1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper.
9 11
10 1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc. 12 1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc.
11 13
97 <option value="loom">Loom format hdf5</option> 99 <option value="loom">Loom format hdf5</option>
98 </param> 100 </param>
99 </xml> 101 </xml>
100 102
101 <xml name="output_object_params"> 103 <xml name="output_object_params">
102 <param name="output_format" argument="--output-format" type="select" label="Format of output object"> 104 <param name="output_format" argument="--output-format" type="select" label="Format of output object" help="AnnData or Loom. Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.">
103 <option value="anndata_h5ad" selected="true">AnnData format</option> 105 <option value="anndata_h5ad" selected="true">AnnData format</option>
104 <option value="anndata">AnnData format (h5 for older versions)</option> 106 <option value="anndata">AnnData format (h5 for older versions)</option>
105 <option value="loom">Loom format</option> 107 <option value="loom">Loom format</option>
106 <option value="loom_legacy">Loom format (h5 for older versions)</option> 108 <option value="loom_legacy">Loom format (h5 for older versions)</option>
109 <option value="no_matrix_output">No packaged matrix output</option>
107 </param> 110 </param>
108 </xml> 111 </xml>
109 112
110 <xml name="output_object_params_no_loom"> 113 <xml name="output_object_params_no_loom">
111 <param name="output_format" argument="--output-format" type="select" label="Format of output object"> 114 <param name="output_format" argument="--output-format" type="select" label="Format of output object" help="Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.">
112 <option value="anndata_h5ad" selected="true">AnnData format</option> 115 <option value="anndata_h5ad" selected="true">AnnData format</option>
113 <option value="anndata">AnnData format (h5 for older versions)</option> 116 <option value="anndata">AnnData format (h5 for older versions)</option>
117 <option value="no_matrix_output">No packaged matrix output (useful for cases where auxiliary files are generated)</option>
114 </param> 118 </param>
115 </xml> 119 </xml>
116 120
117 <xml name="output_data_obj_no_loom" token_description="operation"> 121 <xml name="output_data_obj_no_loom" token_description="operation">
118 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> 122 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
119 <filter>output_format == 'anndata_h5ad'</filter> 123 <filter>output_format == 'anndata_h5ad'</filter>
120 </data> 124 </data>
121 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> 125 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData (h5)">
122 <filter>output_format == 'anndata'</filter> 126 <filter>output_format == 'anndata'</filter>
123 </data> 127 </data>
124 </xml> 128 </xml>
125 129
126 <xml name="output_data_obj" token_description="operation"> 130 <xml name="output_data_obj" token_description="operation">
127 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> 131 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
128 <filter>output_format == 'anndata_h5ad'</filter> 132 <filter>output_format == 'anndata_h5ad'</filter>
129 </data> 133 </data>
130 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> 134 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData (h5)">
131 <filter>output_format == 'anndata'</filter> 135 <filter>output_format == 'anndata'</filter>
132 </data> 136 </data>
133 <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom"> 137 <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
134 <filter>output_format == 'loom_legacy'</filter> 138 <filter>output_format == 'loom_legacy'</filter>
135 </data> 139 </data>
136 <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom"> 140 <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom (h5)">
137 <filter>output_format == 'loom'</filter> 141 <filter>output_format == 'loom'</filter>
138 </data> 142 </data>
139 </xml> 143 </xml>
140 144
141 <xml name="save_matrix_params"> 145 <xml name="save_matrix_params">