Mercurial > repos > ebi-gxa > salmon_kallisto_mtx_to_10x

comparison salmonKallistoMtxTo10x.xml @ 6:17f7e1e51fad draft

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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 c06e0424fd25356d1a8c172fb92b383fd9d28e90
author ebi-gxa
date Thu, 21 Nov 2019 09:38:48 -0500
parents cd6007b47199
children 60fa6080f86f
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5:cd6007b47199 6:17f7e1e51fad
1 <tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy1"> 1 <tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy2">
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>
21 <param name="barcodes_file" type="data" format="txt" label="Tab-delimited barcodes file" /> 21 <param name="barcodes_file" type="data" format="txt" label="Tab-delimited barcodes file" />
22 <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"/> 22 <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"/>
23 </inputs> 23 </inputs>
24 24
25 <outputs> 25 <outputs>
26 <data name="genes_out" format="txt" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/> 26 <data name="genes_out" format="tabular" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/>
27 <data name="barcodes_out" format="txt" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: barcodes"/> 27 <data name="barcodes_out" format="tabular" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: barcodes"/>
28 <data name="matrix_out" format="mtx" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: matrix" /> 28 <data name="matrix_out" format="mtx" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: matrix" />
29 </outputs> 29 </outputs>
30 30
31 <help><![CDATA[ 31 <help><![CDATA[
32 .. class:: infomark 32 .. class:: infomark