Mercurial > repos > ebi-gxa > salmon_kallisto_mtx_to_10x

comparison salmonKallistoMtxTo10x.xml @ 3:336ae8f0a0b2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
date Fri, 08 Nov 2019 08:36:12 -0500
parents 40f7a3d18cf4
children 050b51d0f3c4
comparison
equal deleted inserted replaced
2:40f7a3d18cf4 3:336ae8f0a0b2
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 detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 file $mtx_file | grep 'gzip compressed'; 8 file $mtx_file | grep 'gzip compressed' > /dev/null;
9 if [ $? -eq 0 ]; then 9 if [ $? -eq 0 ]; then
10 matrixfile=matrix.mtx.gz; 10 matrixfile=matrix.mtx.gz;
11 ln -s ${mtx_file} matrix.mtx.gz;
12 else 11 else
13 matrixfile=matrix.mtx; 12 matrixfile=matrix.mtx;
14 fi; 13 fi;
15 ln -s ${mtx_file} \$matrixfile; 14 ln -s ${mtx_file} \$matrixfile;
16 $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./ 15 $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./