annotate dropletutils-read-10x.xml @ 6:ca62f52e0d7f draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:39:58 +0000
parents 3dd08eb96cf6
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="dropletutils_read_10x" name="DropletUtils Read10x" version="@TOOL_VERSION@+galaxy0">
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3 <description>into SingleCellExperiment object</description>
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4 <macros>
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5 <import>dropletutils_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '${matrix}' matrix.mtx &&
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10 ln -s '${genes}' genes.tsv &&
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11 ln -s '${barcodes}' barcodes.tsv &&
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12 dropletutils-read-10x-counts.R
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13 -s .
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14 -c TRUE
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15 -o '${output_rds}'
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16
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17 #if $add_metadata.add_metadata_file
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18 --metadata-files "${add_metadata.metadata_files}"
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19 --cell-id-column "${add_metadata.cell_id_column}"
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20 #end if
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21
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22 ]]></command>
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24 <inputs>
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25 <param name="matrix" type="data" format="txt" label="Expression matrix in sparse matrix format (.mtx)"/>
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26 <param name="genes" type="data" format="tsv,tabular" label="Gene table"/>
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27 <param name="barcodes" type="data" format="tsv,tabular" label="Barcode/cell table"/>
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28 <conditional name="add_metadata">
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29 <param name="add_metadata_file" type="boolean" checked="false" label="Should metadata file be added?" />
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30 <when value="true" >
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31 <param name="metadata_files" type="data" label="Metadata file" help="Provide metadata file e.g. containing cell types"/>
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32 <param name="cell_id_column" type="text" label="Cell ID column" help="Cell ID column. Values must match those provided in the expression matrix." />
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33 </when>
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34 </conditional>
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35 </inputs>
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36
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37 <outputs>
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38 <data name="output_rds" format="rdata" label="${tool.name} on ${on_string}: serialized SingleCellExperiment object"/>
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39 </outputs>
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40
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41 <tests>
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42 <test>
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43 <param name="matrix" value="matrix.mtx"/>
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44 <param name="genes" value="genes.tsv"/>
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45 <param name="barcodes" value="barcodes.tsv"/>
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46 <output name="output_rds" file="raw_sce.rds" ftype="rdata" compare="sim_size" delta="1000000"/>
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47 </test>
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48 </tests>
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49
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50 <help><![CDATA[
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51 =============================================================
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52 Read 10x-Genomics-formatted mtx directory (`Read10xCounts()`)
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53 =============================================================
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54
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55 The mtx directory should contain:
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56
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57 1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell.
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58
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59 2) A gene table of at least two columns where the first column gives the gene IDs.
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60
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61 3) A barcode/cell table of at least one column giving the barcode/cell IDs.
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62
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63 The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval`
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64 with a dataset accession.
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65
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66
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67 @HELP@
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68 ]]></help>
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69 <expand macro="citations"/>
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70 </tool>