Mercurial > repos > iuc > fastk_logex

comparison logex.xml @ 0:387a1695d800 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
author iuc
date Tue, 07 Jan 2025 13:40:08 +0000
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children a919666df221
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-1:000000000000 0:387a1695d800
1 <tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="MIT">
2 <description>Performs binary operations on the generated Ktab files from FASTK suite</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p logex_ktabs
9 && mkdir -p input_files
10 && cp '$input_ktab1' input_files/input1.ktab
11 && ln -s '$input_ktab1_tar' input1.tar
12 && tar -xf input1.tar
13 && mv ktabfiles ktabfiles_in1
14 && mv "\$(find ktabfiles_in1 -type f -name '*.ktab.1')" "ktabfiles_in1/.input1.ktab.1"
15 && cp '$input_ktab2' input_files/input2.ktab
16 && ln -s '$input_ktab2_tar' input2.tar
17 && tar -xf input2.tar
18 && mv ktabfiles ktabfiles_in2
19 && mv "\$(find ktabfiles_in2 -type f -name '*.ktab.1')" "ktabfiles_in2/.input2.ktab.1"
20 && mv ktabfiles_in1/.input1.ktab.1 input_files/
21 && mv ktabfiles_in2/.input2.ktab.1 input_files/ &&
22 #if $operation_selector == 'and':
23 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&.B' input_files/input1.ktab input_files/input2.ktab
24 #elif $operation_selector == 'or':
25 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A|.B' input_files/input1.ktab input_files/input2.ktab
26 #elif $operation_selector == 'minus':
27 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A-B' input_files/input1.ktab input_files/input2.ktab
28 #elif $operation_selector == 'xor':
29 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A^B' input_files/input1.ktab input_files/input2.ktab
30 #elif $operation_selector == 'unionsum':
31 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&+B' input_files/input1.ktab input_files/input2.ktab
32 #end if
33 && cp *.ktab logex_ktabs/
34 && cp .*.ktab* logex_ktabs/
35 && tar -cf logex_ktab.tar input_files/ logex_ktabs/
36 ]]></command>
37 <inputs>
38 <param name="input_ktab1" type="data" format="fastk_ktab" label="Input FastK ktab file (first)"/>
39 <param name="input_ktab1_tar" type="data" format="fastk_ktab" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
40 <param name="input_ktab2" type="data" format="fastk_ktab" label="Input FastK ktab file (second)"/>
41 <param name="input_ktab2_tar" type="data" format="fastk_ktab" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
42 <param name="operation_selector" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files.">
43 <option value="and">AND</option>
44 <option value="or">OR</option>
45 <option value="minus">Minus</option>
46 <option value="unionsum">Unionsum</option>
47 <option value="xor">XOR</option>
48 </param>
49 </inputs>
50 <outputs>
51 <data name="fastk_hist_out" format="fastk_hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Logex .hist file"/>
52 <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="out.ktab" label="${tool.name} on ${on_string}: Logex .ktab file"/>
53 <data name="fastk_ktab_files" format="tar" from_work_dir="logex_ktab.tar" label="${tool.name} on ${on_string}: FastK Logex ktab files"/>
54 </outputs>
55 <tests>
56 <test expect_num_outputs="3">
57 <param name="input_ktab1" value="fastq1.ktab"/>
58 <param name="input_ktab1_tar" value="fastk_in1.tar"/>
59 <param name="input_ktab2" value="fastq2.ktab"/>
60 <param name="input_ktab2_tar" value="fastk_in2.tar"/>
61 <param name="operation_selector" value="AND"/>
62 <output name="fastk_hist_out" ftype="fastk_hist">
63 <assert_contents>
64 <has_size value="262164"/>
65 </assert_contents>
66 </output>
67 <output name="fastk_ktab_out" ftype="fastk_ktab">
68 <assert_contents>
69 <has_size value="2064"/>
70 </assert_contents>
71 </output>
72 <output name="fastk_ktab_files" ftype="tar">
73 <assert_contents>
74 <has_archive_member path="logex_ktabs/out.ktab"/>
75 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
76 <has_archive_member path="input_files/input1.ktab"/>
77 <has_archive_member path="input_files/.input1.ktab.1"/>
78 <has_archive_member path="input_files/input2.ktab"/>
79 <has_archive_member path="input_files/.input2.ktab.1"/>
80 </assert_contents>
81 </output>
82 </test>
83 </tests>
84 <help><![CDATA[
85
86 Logex tool can perform operations such as AND, OR, XOR, Minus and Unionsum on the input given input Ktab files.
87
88 The tool requires two input Ktab files and their associated files (Generated in the tarball of FASTK tool with .1 extension) as inputs to perform various binary operations.
89
90 ]]></help>
91 <expand macro="citations"/>
92 </tool>