Mercurial > repos > jjohnson > arriba

annotate arriba_get_filters.xml @ 8:1a56888ddb7d draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit f5af83950615d8c77a3a43cf45f5ddf46000701b"
author jjohnson
date Mon, 11 Oct 2021 19:00:45 +0000
parents 005b200c8841
children
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1 <tool id="arriba_get_filters" name="Arriba Get Filters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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2 <description>to history</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
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10 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
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11 REF_DIR=\$(dirname \$REF_SCRIPT) &&
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12 REF_NAME=${arriba_reference_name.split('+')[0].replace('viral','')} &&
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13 echo \$REF_NAME &&
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14 cp `find \$REF_DIR -name 'blacklist_*' | grep -i \$REF_NAME` '$blacklist' &&
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15 cp `find \$REF_DIR -name 'known_fusions_*' | grep -i \$REF_NAME` '$known_fusions' &&
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16 cp `find \$REF_DIR -name 'protein_domains_*' | grep -i \$REF_NAME` '$protein_domains' &&
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17 cp `find \$REF_DIR -name 'cytobands_*' | grep -i \$REF_NAME` '$cytobands'
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18 #*
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19 cp "\$REF_DIR/blacklist_*${arriba_reference_name}*" '$blacklist' &&
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20 cp "\$REF_DIR/known_fusions_*${arriba_reference_name}*" '$known_fusions' &&
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21 cp "\$REF_DIR/protein_domains_*${arriba_reference_name}*" '$protein_domains' &&
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22 cp "\$REF_DIR/cytobands_*${arriba_reference_name}*" '$cytobands'
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23 *#
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24 ]]></command>
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25 <inputs>
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26 <param name="arriba_reference_name" type="text" label="Select reference">
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27 <help>GRCh38 GRCh37 hg38 hg19 GRCm38 mm10</help>
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28 <option value="GRCh38">GRCh38</option>
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29 <option value="GRCh37">GRCh37</option>
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30 <option value="hg38">hg38</option>
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31 <option value="hg19">hg19</option>
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32 <option value="GRCm38">GRCm38</option>
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33 <option value="mm10">mm10</option>
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34 </param>
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35 </inputs>
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36 <outputs>
5
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37 <data name="blacklist" format="tabular.gz" label="${tool.name} ${arriba_reference_name} blacklist.tsv.gz"/>
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38 <data name="known_fusions" format="tabular.gz" label="${tool.name} ${arriba_reference_name} known_fusions.tsv.gz"/>
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39 <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/>
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40 <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/>
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41 </outputs>
4
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42 <tests>
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43 <test>
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44 <param name="arriba_reference_name" value="GRCh38"/>
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45 <output name="cytobands">
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46 <assert_contents>
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47 <has_text_matching expression="1\t1\t\d+\tp36.33\tgneg"/>
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48 </assert_contents>
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49 </output>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53 **Arriba Get Filters**
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54
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55 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
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56 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
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57
5
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58 The **Arriba Get Filters** tool adds the following Arriba distribution input_files_ to your galaxy history:
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59
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60 - blacklist
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61 - known_fusions
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62 - protein_domains
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63 - cytobands
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64
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65
2
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66 .. _Arriba: https://arriba.readthedocs.io/en/latest/
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67 .. _input_files: https://arriba.readthedocs.io/en/latest/input-files/
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68
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69 ]]></help>
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70 <expand macro="citations" />
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71 </tool>