Mercurial > repos > jjohnson > arriba

annotate arriba_get_filters.xml @ 4:77021ad5037d draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
author jjohnson
date Sat, 09 Oct 2021 15:41:49 +0000
parents 7420753b0671
children 005b200c8841
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7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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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">
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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2 <description>to history</description>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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3 <macros>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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4 <import>macros.xml</import>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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5 </macros>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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6 <expand macro="requirements" />
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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7 <expand macro="version_command" />
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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8 <command detect_errors="exit_code"><![CDATA[
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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9 BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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10 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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11 REF_DIR=\$(dirname \$REF_SCRIPT) &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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12 REF_NAME=${arriba_reference_name.split('+')[0].replace('viral','')} &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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13 echo \$REF_NAME &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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14 cp `find \$REF_DIR -name 'blacklist_*' | grep -i \$REF_NAME` '$blacklist' &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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15 cp `find \$REF_DIR -name 'known_fusions_*' | grep -i \$REF_NAME` '$known_fusions' &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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16 cp `find \$REF_DIR -name 'protein_domains_*' | grep -i \$REF_NAME` '$protein_domains' &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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17 cp `find \$REF_DIR -name 'cytobands_*' | grep -i \$REF_NAME` '$cytobands'
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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18 #*
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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19 cp "\$REF_DIR/blacklist_*${arriba_reference_name}*" '$blacklist' &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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20 cp "\$REF_DIR/known_fusions_*${arriba_reference_name}*" '$known_fusions' &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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21 cp "\$REF_DIR/protein_domains_*${arriba_reference_name}*" '$protein_domains' &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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22 cp "\$REF_DIR/cytobands_*${arriba_reference_name}*" '$cytobands'
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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23 *#
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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24 ]]></command>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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25 <inputs>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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26 <param name="arriba_reference_name" type="text" label="Select reference">
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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27 <help>GRCh38 GRCh37 hg38 hg19 GRCm38 mm10</help>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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28 <option value="GRCh38">GRCh38</option>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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29 <option value="GRCh37">GRCh37</option>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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30 <option value="hg38">hg38</option>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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31 <option value="hg19">hg19</option>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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32 <option value="GRCm38">GRCm38</option>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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33 <option value="mm10">mm10</option>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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34 </param>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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35 </inputs>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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36 <outputs>
4
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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37 <data name="blacklist" format="tabular" label="${tool.name} ${arriba_reference_name} blacklist.tsv"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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38 <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions.tsv"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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39 <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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40 <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/>
2
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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"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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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>
2
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52 <help><![CDATA[
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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53 ** Arriba **
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54
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
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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
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58 .. _Arriba: https://arriba.readthedocs.io/en/latest/
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59
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60 ]]></help>
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61 <expand macro="citations" />
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62 </tool>