Mercurial > repos > ebi-gxa > salmon_kallisto_mtx_to_10x
comparison salmonKallistoMtxTo10x.xml @ 1:a2aaefceb418 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 3fbbd818012005da4513271beda50df98d3c1cde-dirty
author | ebi-gxa |
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date | Fri, 08 Nov 2019 08:09:09 -0500 |
parents | fe0fd27aba50 |
children | 40f7a3d18cf4 |
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0:fe0fd27aba50 | 1:a2aaefceb418 |
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1 <tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy0"> | 1 <tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy1"> |
2 <description>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</description> | 2 <description>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package">scipy</requirement> | 4 <requirement type="package">scipy</requirement> |
5 <requirement type="package">pandas</requirement> | 5 <requirement type="package">pandas</requirement> |
6 </requirements> | 6 </requirements> |
7 <command interpreter="python" detect_errors="exit_code"><![CDATA[ | 7 <command interpreter="python" detect_errors="exit_code"><![CDATA[ |
8 $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./ | 8 $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./ |
9 ]]></command> | 9 ]]></command> |
10 | 10 |
11 <inputs> | 11 <inputs> |
12 <param name="mtx_file" type="data" format="txt" label=".mtx-format matrix" /> | 12 <param name="mtx_file" type="data" format="mtx" label=".mtx-format matrix" /> |
13 <param name="genes_file" type="data" format="txt" label="Tab-delimited genes file" /> | 13 <param name="genes_file" type="data" format="txt" label="Tab-delimited genes file" /> |
14 <param name="barcodes_file" type="data" format="txt" label="Tab-delimited barcodes file" /> | 14 <param name="barcodes_file" type="data" format="txt" label="Tab-delimited barcodes file" /> |
15 <param name="cell_prefix" type="text" optional='true' value="" label="Prefix to prepend to cell names / barcodes" help="This is useful when multiple matrices from different libraries with overlapping barcodes will be merged"/> | 15 <param name="cell_prefix" type="text" optional='true' value="" label="Prefix to prepend to cell names / barcodes" help="This is useful when multiple matrices from different libraries with overlapping barcodes will be merged"/> |
16 </inputs> | 16 </inputs> |
17 | 17 |
18 <outputs> | 18 <outputs> |
19 <data name="genes_out" format="txt" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/> | 19 <data name="genes_out" format="txt" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/> |
20 <data name="barcodes_out" format="txt" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: barcodes"/> | 20 <data name="barcodes_out" format="txt" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: barcodes"/> |
21 <data name="matrix_out" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: matrix" /> | 21 <data name="matrix_out" format="mtx" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: matrix" /> |
22 </outputs> | 22 </outputs> |
23 | 23 |
24 <help><![CDATA[ | 24 <help><![CDATA[ |
25 .. class:: infomark | 25 .. class:: infomark |
26 | 26 |