Mercurial > repos > jjohnson > arriba_get_filters
comparison arriba_get_filters.xml @ 0:463dd21dc267 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
author | jjohnson |
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date | Fri, 11 Feb 2022 19:08:51 +0000 |
parents | |
children | f1e60cf0823a |
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-1:000000000000 | 0:463dd21dc267 |
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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"> | |
2 <description>to history</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <expand macro="version_command" /> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 BASE_DIR=\$(dirname \$(dirname `which arriba`)) && | |
10 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` && | |
11 REF_DIR=\$(dirname \$REF_SCRIPT) && | |
12 REF_NAME=${arriba_reference_name.split('+')[0].replace('viral','')} && | |
13 echo \$REF_NAME && | |
14 cp `find \$REF_DIR -name 'blacklist_*' | grep -i \$REF_NAME` '$blacklist' && | |
15 cp `find \$REF_DIR -name 'known_fusions_*' | grep -i \$REF_NAME` '$known_fusions' && | |
16 cp `find \$REF_DIR -name 'protein_domains_*' | grep -i \$REF_NAME` '$protein_domains' && | |
17 cp `find \$REF_DIR -name 'cytobands_*' | grep -i \$REF_NAME` '$cytobands' | |
18 #* | |
19 cp "\$REF_DIR/blacklist_*${arriba_reference_name}*" '$blacklist' && | |
20 cp "\$REF_DIR/known_fusions_*${arriba_reference_name}*" '$known_fusions' && | |
21 cp "\$REF_DIR/protein_domains_*${arriba_reference_name}*" '$protein_domains' && | |
22 cp "\$REF_DIR/cytobands_*${arriba_reference_name}*" '$cytobands' | |
23 *# | |
24 ]]></command> | |
25 <inputs> | |
26 <param name="arriba_reference_name" type="text" label="Select reference"> | |
27 <help>GRCh38 GRCh37 hg38 hg19 GRCm38 mm10</help> | |
28 <option value="GRCh38">GRCh38</option> | |
29 <option value="GRCh37">GRCh37</option> | |
30 <option value="hg38">hg38</option> | |
31 <option value="hg19">hg19</option> | |
32 <option value="GRCm38">GRCm38</option> | |
33 <option value="mm10">mm10</option> | |
34 </param> | |
35 </inputs> | |
36 <outputs> | |
37 <data name="blacklist" format="tabular.gz" label="${tool.name} ${arriba_reference_name} blacklist.tsv.gz"/> | |
38 <data name="known_fusions" format="tabular.gz" label="${tool.name} ${arriba_reference_name} known_fusions.tsv.gz"/> | |
39 <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/> | |
40 <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/> | |
41 </outputs> | |
42 <tests> | |
43 <test> | |
44 <param name="arriba_reference_name" value="GRCh38"/> | |
45 <output name="cytobands"> | |
46 <assert_contents> | |
47 <has_text_matching expression="1\t1\t\d+\tp36.33\tgneg"/> | |
48 </assert_contents> | |
49 </output> | |
50 </test> | |
51 </tests> | |
52 <help><![CDATA[ | |
53 **Arriba Get Filters** | |
54 | |
55 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. | |
56 It is based on chimeric alignments found by the STAR RNA-Seq aligner. | |
57 | |
58 The **Arriba Get Filters** tool adds the following Arriba distribution input_files_ to your galaxy history: | |
59 | |
60 - blacklist | |
61 - known_fusions | |
62 - protein_domains | |
63 - cytobands | |
64 | |
65 | |
66 .. _Arriba: https://arriba.readthedocs.io/en/latest/ | |
67 .. _input_files: https://arriba.readthedocs.io/en/latest/input-files/ | |
68 | |
69 ]]></help> | |
70 <expand macro="citations" /> | |
71 </tool> |