Mercurial > repos > ebi-gxa > salmon_kallisto_mtx_to_10x

comparison salmonKallistoMtxTo10x.xml @ 10:88f5a0a6a818 draft default tip

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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 ec0f8964f4b64fa4d63fba73b9622d7f70b24285
author ebi-gxa
date Wed, 11 May 2022 12:55:40 +0000
parents e42c217a450f
children
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9:e42c217a450f 10:88f5a0a6a818
1 <tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy5" profile="18.01"> 1 <tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy6" profile="18.01">
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" version="1.4.1">scipy</requirement> 4 <requirement type="package" version="1.4.1">scipy</requirement>
5 <requirement type="package" version="1.0.1">pandas</requirement> 5 <requirement type="package" version="1.0.1">pandas</requirement>
6 <requirement type="package" version="5.37">file</requirement> 6 <requirement type="package" version="5.37">file</requirement>
7 </requirements> 7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 file $mtx_file | grep 'gzip compressed' > /dev/null; 9 file $mtx_file | grep 'gzip compressed' > /dev/null;
10 if [ $? -eq 0 ]; then 10 if [ $? -eq 0 ]; then
11 matrixfile=matrix.mtx.gz; 11 matrixfile=matrix-in.mtx.gz;
12 else 12 else
13 matrixfile=matrix.mtx; 13 matrixfile=matrix-in.mtx;
14 fi; 14 fi;
15 ln -s ${mtx_file} \$matrixfile; 15 ln -s ${mtx_file} \$matrixfile;
16 $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "\${matrixfile}" "${genes_file}" "${barcodes_file}" ./ 16 $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "\${matrixfile}" "${genes_file}" "${barcodes_file}" ./
17 ]]></command> 17 ]]></command>
18 18
64 title = {Hinxton Single Cell Anlysis Environment}, 64 title = {Hinxton Single Cell Anlysis Environment},
65 publisher = {GitHub}, 65 publisher = {GitHub},
66 journal = {GitHub repository}, 66 journal = {GitHub repository},
67 url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary}, 67 url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary},
68 }</citation> 68 }</citation>
69 <citation type="doi">10.1101/2020.04.08.032698</citation>
69 </citations> 70 </citations>
70 </tool> 71 </tool>