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comparison arriba_get_filters.xml @ 2:7420753b0671 draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
author jjohnson
date Fri, 08 Oct 2021 19:23:48 +0000
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children 77021ad5037d
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1:9f2665b32c45 2:7420753b0671
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}*" '$cytobands'
23 *#
24 ]]></command>
25 <inputs>
26 <param name="arriba_reference_name" type="text" label="Select reference">
27 <help>GRCh38 GRCh37 hg38 hg19 GRCm38 mm10</help>
28 <option value="GRCh38">GRCh38</option>
29 <option value="GRCh37">GRCh37</option>
30 <option value="hg38">hg38</option>
31 <option value="hg19">hg19</option>
32 <option value="GRCm38">GRCm38</option>
33 <option value="mm10">mm10</option>
34 </param>
35 </inputs>
36 <outputs>
37 <data name="blacklist" format="tabular" label="${tool.name} ${arriba_reference_name} blacklist"/>
38 <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions"/>
39 <data name="protein_domains" format="tabular" label="${tool.name} ${arriba_reference_name} protein_domains"/>
40 <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands"/>
41 </outputs>
42 <help><![CDATA[
43 ** Arriba **
44
45 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
46 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
47
48 .. _Arriba: https://arriba.readthedocs.io/en/latest/
49
50 ]]></help>
51 <expand macro="citations" />
52 </tool>