Mercurial > repos > ebi-gxa > gtf2gene_list
annotate gtf2gene_list.xml @ 0:040d4b3a19d5 draft
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author | ebi-gxa |
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date | Wed, 03 Apr 2019 12:05:26 -0400 |
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040d4b3a19d5
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy0"> |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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2 <description>extracts gene ids from Ensembl GTF using rtracklayer</description> |
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3 <requirements> |
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4 <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement> |
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5 </requirements> |
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6 <command detect_errors="exit_code"><![CDATA[ |
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7 ln -s '$gtf_input' input.gtf; |
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8 Rscript $__tool_directory__/gtf2gene.R input.gtf |
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9 ]]></command> |
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10 |
040d4b3a19d5
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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11 <inputs> |
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12 <param name="gtf_input" type="data" format="gff" label="Ensembl GTF file" /> |
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13 </inputs> |
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14 |
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15 <outputs> |
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16 <data name="gene_list" format="tsv" from_work_dir="genes.txt" label="${tool.name} on ${on_string}"/> |
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17 </outputs> |
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18 <tests> |
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19 <test> |
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20 <param name="gtf_input" ftype="data" value="short_ensembl_gtf.gtf"/> |
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21 <output name="gene_list" ftype="data" value="genes.txt" compare="sim_size"/> |
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22 </test> |
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23 </tests> |
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24 |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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25 |
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26 <help><![CDATA[ |
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27 .. class:: infomark |
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28 |
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29 **What it does** |
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30 |
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31 Given an Ensembl GTF file, it will extract the list of all gene identifiers in the GTF to a simple tsv file. |
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32 |
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33 **Inputs** |
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34 |
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35 * Ensembl GTF file |
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36 |
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37 ----- |
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38 |
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39 **Outputs** |
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40 |
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41 * Gene identifier list in tsv. |
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42 ]]></help> |
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43 <citations> |
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44 <citation type="bibtex"> |
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45 @misc{github-hinxton-single-cell, |
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46 author = {Pablo Moreno, EBI Gene Expression Team}, |
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47 year = {2019}, |
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48 title = {Hinxton Single Cell Anlysis Environment}, |
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49 publisher = {GitHub}, |
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50 journal = {GitHub repository}, |
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51 url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary}, |
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52 }</citation> |
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53 </citations> |
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54 </tool> |