Mercurial > repos > ebi-gxa > salmon_kallisto_mtx_to_10x

comparison salmonKallistoMtxTo10x.xml @ 8:5675dc87bb8d 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 bf9021c853da640771202920cde38f77cdeaf368"
author ebi-gxa
date Wed, 04 Mar 2020 06:44:57 -0500
parents 60fa6080f86f
children e42c217a450f
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equal deleted inserted replaced
7:60fa6080f86f 8:5675dc87bb8d
1 <tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy3"> 1 <tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy4" 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">scipy</requirement> 4 <requirement type="package" version="1.4.1">scipy</requirement>
5 <requirement type="package">pandas</requirement> 5 <requirement type="package" version="1.0.1">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' > /dev/null; 8 file $mtx_file | grep 'gzip compressed' > /dev/null;
9 if [ $? -eq 0 ]; then 9 if [ $? -eq 0 ]; then
10 matrixfile=matrix.mtx.gz; 10 matrixfile=matrix.mtx.gz;
25 <outputs> 25 <outputs>
26 <data name="genes_out" format="tabular" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/> 26 <data name="genes_out" format="tabular" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/>
27 <data name="barcodes_out" format="tabular" from_work_dir="barcodes.tsv" label="${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
33 33
34 **What it does** 34 **What it does**
35 35
37 37
38 **Inputs** 38 **Inputs**
39 39
40 MTX and row and gene labels from the relevant tool. For Alevin this will be 40 MTX and row and gene labels from the relevant tool. For Alevin this will be
41 41
42 * Matrix file: quants_mat.mtx.gz 42 * Matrix file: quants_mat.mtx.gz
43 * Genes file: quants_mat_cols.txt 43 * Genes file: quants_mat_cols.txt
44 * Barcodes file: quants_mat_rows.txt 44 * Barcodes file: quants_mat_rows.txt
45 45
46 For Kallisto it will be: 46 For Kallisto it will be:
47 47
48 * Matrix file: [name].mtx.gz 48 * Matrix file: [name].mtx.gz
49 * Genes file: [name].genes.txt 49 * Genes file: [name].genes.txt
50 * Barcodes file: [name].barcodes.txt 50 * Barcodes file: [name].barcodes.txt
51 51
52 ----- 52 -----
53 53