Mercurial > repos > ebi-gxa > seurat_export_cellbrowser

comparison seurat_export_cellbrowser.xml @ 3:d0ab20c5b81d draft default tip

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planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
author ebi-gxa
date Sun, 01 Oct 2023 09:06:07 +0000
parents 6e876c9925c5
children
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2:6e876c9925c5 3:d0ab20c5b81d
1 <tool id="seurat_export_cellbrowser" name="Seurat Export2CellBrowser" version="@SEURAT_VERSION@_@VERSION@+galaxy0"> 1 <tool id="seurat_export_cellbrowser" name="Seurat Export2CellBrowser" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
2 <description>produces files for UCSC CellBrowser import.</description> 2 <description>produces files for UCSC CellBrowser import.</description>
3 <macros> 3 <macros>
4 <import>seurat_macros.xml</import> 4 <import>seurat_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
22 cd output_html && tar -cf '$output' *; 22 cd output_html && tar -cf '$output' *;
23 ]]></command> 23 ]]></command>
24 24
25 <inputs> 25 <inputs>
26 <expand macro="input_object_params"/> 26 <expand macro="input_object_params"/>
27 <param name="markers_file" type="data" format="txt" label="Marker genes file from Seurat" /> 27 <param name="markers_file" type="data" optional="True" format="txt" label="Marker genes file from Seurat" />
28 </inputs> 28 </inputs>
29 29
30 <outputs> 30 <outputs>
31 <data name="output" format="tar" label="${tool.name} on ${on_string}: UCSC CellBrowser bundle"/> 31 <data name="output" format="tar" label="${tool.name} on ${on_string}: UCSC CellBrowser bundle"/>
32 </outputs> 32 </outputs>
33 33
34 <tests> 34 <tests>
35 <test> 35 <test>
36 <param name="rds_input" ftype="rdata" value="out_runtsne.rds"/> 36 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-tsne.rds"/>
37 <param name="markers_file" ftype="txt" value="out_markers.csv"/> 37 <param name="markers_file" ftype="txt" value="E-MTAB-6077-3k_features_90_cells-markers.csv"/>
38 <output name="output" ftype="tar" value="out_cellbrowser_bundle.tar"/> 38 <output name="output" >
39 <assert_contents>
40 <has_size value="2182656" delta="200000"/>
41 </assert_contents>
42 </output>
39 </test> 43 </test>
40 </tests> 44 </tests>
41 <help><![CDATA[ 45 <help><![CDATA[
42 .. class:: infomark 46 .. class:: infomark
43 47