Mercurial > repos > spanish_national_institue_of_bioinformatics > biobb

annotate nucDyn_stats.xml @ 0:fa06ddcae68e draft

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author spanish_national_institue_of_bioinformatics
date Thu, 11 Apr 2019 04:01:48 -0400
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1 <tool id="nucDyn_stats" name="Nucleosome Dynamics Statistics" version="0.1">
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2 <description>: statistics on Nucleosome Dynamics analysis</description>
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3 <requirements>
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4 <requirement type="binary">docker</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 ln -f -s $output_gw_png_file $output_gw_png_file\.png;
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9 docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucldyn nucDyn_stats --input $gff_file
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10 #if $assembly.source == "buildin":
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11 --genome ${assembly.ref_genome_gff_buildin}
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12 #else if $assembly.source == "history":
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13 --genome ${assembly.ref_genome_gff_history}
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14 #end if
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15 --out_genes $output_genes_csv_file --out_gw $output_gw_png_file\.png;
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16 rm $output_gw_png_file\.png
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="gff_file" type="data" format="gff" label="Input Nucleosome Calls"/>
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21 <conditional name="assembly">
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22 <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their chromosome sizes and their annotated genes.">
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23 <option value="buildin" selected="True">Use a built-in genome</option>
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24 <option value="history">Use a genome from the history</option>
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25 </param>
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26 <when value="buildin">
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27 <param name="ref_genome_gff_buildin" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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28 <options from_file="nucldyn_publicdata.loc">
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29 <column name="name" index="2"/>
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30 <column name="value" index="4"/>
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31 </options>
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32 </param>
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33 </when>
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34 <when value="history">
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35 <param name="ref_genome_gff_history" type="data" format="gff" label="Select gene annotations for your reference genome" help="Check below the documentation for lerning about the file format."/>
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36 </when>
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37 </conditional>
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38 </inputs>
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39 <outputs>
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40 <data format="csv" name="output_genes_csv_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" />
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41 <data format="png" name="output_gw_png_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.png" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="gff_file" value="ND__cellcycleG2_chrII_cellcycleM_chrII.gff" />
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46 <param name="ref_genome_gff_buildin" value="genes.gff" />
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47 <output name="output_genes_csv_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv" />
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48 <output name="output_gw_png_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png" />
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49 </test>
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50 </tests>
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51 <help>
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52 .. class:: warningmark
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53
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54
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55 Check the documentation for setting the tool parameters at the source code repository: http://mmb.irbbarcelona.org/gitlab/NuclDynamics/docker
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56
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57 -----
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58
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59 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
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60 :height: 80
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61 :width: 200
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62
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63 **http://mmb.irbbarcelona.org/NucleosomeDynamics**
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64 </help>
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65 <citations>
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66 <citation type="bibtex">
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67 @misc{github,
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68 author = {Buitrago D},
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69 year = {2019},
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70 title = {Nucleosome Dynamics suite: containerized installation},
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71 publisher = {GitLab},
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72 journal = {GitLab repository},
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73 url = {http://mmb.irbbarcelona.org/gitlab/NuclDynamics/docker},
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74 }</citation>
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75 </citations>
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76 </tool>