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comparison read_extractor.xml @ 0:c114d334c67b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
author iuc
date Fri, 03 Dec 2021 23:10:39 +0000
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1 <tool id="megan_read_extractor" name="MEGAN: Extract reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>by classification</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 #set input_identifier = 'input.' + $input.ext.upper()
10 ln -s '${input}' '${input_identifier}' &&
11
12 read-extractor
13 --input '${input_identifier}'
14 #if $frameShiftCorrect:
15 --frameShiftCorrect '$frameShiftCorrect'
16 #end if
17 #if str($specify_classification_cond.specify_classification) == 'yes':
18 --classification '$specify_classification_cond.classification'
19 #if str($specify_classification_cond.specify_classification) == 'yes':
20 #if $specify_classification_cond.classNames:
21 --classNames '$specify_classification_cond.classNames'
22 #end if
23 #end if
24 #else:
25 --all
26 #end if
27 #if $ignoreExceptions:
28 --ignoreExceptions '$ignoreExceptions'
29 #end if
30 --gzipOutputFiles 'false'
31 ## Output must be a directory.
32 --output ./output.txt
33 && mv ./output.txt '${output}'
34 ]]></command>
35 <inputs>
36 <param name="input" argument="--input" type="data" format="daa,rma6" label="Input file"/>
37 <param argument="--frameShiftCorrect" type="boolean" truevalue="true" falsevalue="" checked="false" label="Extract frame-shift corrected reads?" help="Set to Yes only if blast mode of input is BlastX"/>
38 <conditional name="specify_classification_cond">
39 <param name="specify_classification" type="select" label="Specify classification to use?">
40 <option value="yes" selected="true">Yes</option>
41 <option value="no">No</option>
42 </param>
43 <when value="yes">
44 <param argument="--classification" type="select" label="Select classification to use">
45 <expand macro="classification_options"/>
46 </param>
47 <param argument="--classNames" type="text" value="" label="Names (or ids) of classes from which to extract reads" help="Leave blank to extract all classes">
48 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
49 </param>
50 </when>
51 <when value="no"/>
52 </conditional>
53
54 <param argument="--ignoreExceptions" type="boolean" truevalue="true" falsevalue="" checked="false" label="Ignore exceptions and continue processing?"/>
55 </inputs>
56 <outputs>
57 <data name="output" format="txt"/>
58 </outputs>
59 <tests>
60 <test expect_num_outputs="1">
61 <param name="input" value="read_extractor_input.rma6" ftype="rma6"/>
62 <param name="specify_classification" value="no"/>
63 <output name="output" file="read_extractor_output.txt" ftype="txt"/>
64 </test>
65 <test expect_num_outputs="1">
66 <param name="input" value="read_extractor_input.rma6" ftype="rma6"/>
67 <param name="classification" value="Taxonomy"/>
68 <param name="ignoreExceptions" value="true"/>
69 <output name="output" ftype="txt">
70 <assert_contents>
71 <has_size value="0"/>
72 </assert_contents>
73 </output>
74 </test>
75 <test expect_failure="true">
76 <param name="input" value="read_extractor_input.rma6" ftype="rma6"/>
77 <param name="classification" value="EGGNOG"/>
78 <assert_stderr>
79 <has_text text="Input file does not contain the requested classification 'EGGNOG'"/>
80 </assert_stderr>
81 </test>
82 <test expect_failure="true">
83 <param name="input" value="read_extractor_input.rma6" ftype="rma6"/>
84 <param name="frameShiftCorrect" value="true"/>
85 <param name="specify_classification" value="no"/>
86 <assert_stderr>
87 <has_text text="Frame-shift correction only possible when BlastMode is BLASTX"/>
88 </assert_stderr>
89 </test>
90 </tests>
91 <help>
92 **What it does**
93
94 Extracts reads from a DAA or RMA file by classification. This tool accepts the following input data formats.
95
96 * **Direct Access Archive (DAA)** - a proprietary file format developed by PowerISO Computing for disk image files
97 * RealMedia Audio (RMA)** - a proprietary multimedia container format created by RealNetworks. MEGAN uses an update of the original RMA file format known as RMA6 which requires less disk space for files.
98
99 This tool outputs a text file containing the reads.
100
101 </help>
102 <expand macro="citations"/>
103 </tool>
104