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comparison daa2info.xml @ 0:2f8df8e575f2 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 23:09:26 +0000
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-1:000000000000 0:2f8df8e575f2
1 <tool id="megan_daa2info" name="MEGAN: Get information" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>about a DIAMOND file</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}' '${input_identifier}' &&
11
12 daa2info
13 --in '${input_identifier}'
14 #if str($input_is_meganized_cond.input_is_meganized) == 'yes':
15 --listMore
16 #if str($input_is_meganized_cond.list_class2count_cond.list_class2count) == 'yes':
17 --class2count '$input_is_meganized_cond.list_class2count_cond.class2count'
18 $input_is_meganized_cond.list_class2count_cond.sum
19 #end if
20 #if str($input_is_meganized_cond.list_read2class_cond.list_read2class) == 'yes':
21 --read2class '$input_is_meganized_cond.list_read2class_cond.read2class'
22 #end if
23 $input_is_meganized_cond.names
24 $input_is_meganized_cond.paths
25 $input_is_meganized_cond.prefixRank
26 $input_is_meganized_cond.majorRanksOnly
27 #if str($input_is_meganized_cond.bo_or_vo) != 'do_not_restrict':
28 $input_is_meganized_cond.bo_or_vo
29 #end if
30 $input_is_meganized_cond.ignoreUnassigned
31 #else:
32 --list
33 #end if
34 #if $extractSummaryFile:
35 --extractSummaryFile '$output_summary'
36 #end if
37 --out '${output}'
38 ]]></command>
39 <inputs>
40 <param name="input" argument="--in" type="data" format="daa" label="Input DIAMOND file"/>
41 <conditional name="input_is_meganized_cond">
42 <param name="input_is_meganized" type="select" checked="false" label="Input is meganized?" help="Implies the input file was produced by the MEGAN: DAA Meganizer tool">
43 <option value="no" selected="true">No</option>
44 <option value="yes">Yes</option>
45 </param>
46 <when value="no"/>
47 <when value="yes">
48 <conditional name="list_class2count_cond">
49 <param name="list_class2count" type="select" label="List class to count for named classification(s)?">
50 <option value="no" selected="true">No</option>
51 <option value="yes">Yes</option>
52 </param>
53 <when value="no"/>
54 <when value="yes">
55 <param argument="--class2count" type="select" label="Select class to count for named classification(s)">
56 <expand macro="classification_options"/>
57 </param>
58 <param argument="--sum" type="boolean" truevalue="--sum" falsevalue="" checked="false" label="Use summarized rather than assigned counts when listing class to count?"/>
59 </when>
60 </conditional>
61 <conditional name="list_read2class_cond">
62 <param name="list_read2class" type="boolean" truevalue="true" falsevalue="false" checked="false" label="List read to class assignments for named classification(s)?"/>
63 <when value="false"/>
64 <when value="true">
65 <param argument="--read2class" type="select" label="Select read to class assignments for named classification(s)">
66 <expand macro="classification_options"/>
67 </param>
68 </when>
69 </conditional>
70 <param argument="--names" type="boolean" truevalue="--names" falsevalue="" checked="false" label="Report class names rather than class Id numbers?"/>
71 <param argument="--paths" type="boolean" truevalue="--paths" falsevalue="" checked="false" label="Report class paths rather than class Id numbers?"/>
72 <param argument="--prefixRank" type="boolean" truevalue="--prefixRank" falsevalue="" checked="false" label="When reporting class paths for taxonomy, prefix single letter to indicate taxonomic rank?"/>
73 <param argument="--majorRanksOnly" type="boolean" truevalue="--majorRanksOnly" falsevalue="" checked="false" label="Only use major taxonomic ranks?"/>
74 <param name="bo_or_vo" type="select" label="Restrict reporting to either bacterial reads or viral reads in taxonomic report">
75 <option value="do_not_restrict" selected="true">Do not restrict</option>
76 <option value="--bacteriaOnly" selected="true">Bacterial reads and counts</option>
77 <option value="--virusOnly">Viral reads and counts</option>
78 </param>
79 <param argument="--ignoreUnassigned" type="boolean" truevalue="--ignoreUnassigned" falsevalue="" checked="true" label="Don't report on reads that are unassigned?"/>
80 </when>
81 </conditional>
82 <param argument="--extractSummaryFile" type="boolean" truevalue="--extractSummaryFile" falsevalue="" checked="false" label="Output a MEGAN summary file?" help="Contains all classifications, but no reads or alignments"/>
83 </inputs>
84 <outputs>
85 <data name="output" format="txt"/>
86 <data name="output_summary" format="txt" label="${tool.name} on ${on_string} (MEGAN summary)">
87 <filter>extractSummaryFile</filter>
88 </data>
89 </outputs>
90 <tests>
91 <test expect_num_outputs="1">
92 <param name="input" value="input.daa" ftype="daa"/>
93 <output name="output" file="daa2info_output1.txt" ftype="txt" compare="contains"/>
94 </test>
95 <test expect_num_outputs="1">
96 <param name="input" value="input_meganized.daa" ftype="daa"/>
97 <param name="input_is_meganized" value="yes"/>
98 <output name="output" file="daa2info_output2.txt" ftype="txt" compare="contains"/>
99 </test>
100 <test expect_num_outputs="2">
101 <param name="input" value="input_meganized.daa" ftype="daa"/>
102 <param name="input_is_meganized" value="yes"/>
103 <param name="bo_or_vo" value="--virusOnly"/>
104 <param name="extractSummaryFile" value="true"/>
105 <output name="output" file="daa2info_output2.txt" ftype="txt" compare="contains"/>
106 <output name="output_summary" file="daa2info_output_summary2.txt" ftype="txt" compare="contains"/>
107 </test>
108 </tests>
109 <help>
110 **What it does**
111
112 Analyses a DIAMOND (i.e., a Direct Access Archive or DAA) file, a proprietary file format developed by PowerISO Computing
113 for disk image files, and outputs a text file containing information about the file. The information includes the following.
114
115 * Number of reads
116 * Alignment mode
117 * Whether the file is meganized
118 * Classifications
119
120 If the DIAMOND file is meganized (i.e., it was produced by the MEGAN: DAA Meganizer tool), a summary that includes the
121 following information (among other items) is included in the output.
122
123 * Content type
124 * Names
125 * Uids
126 * Sizes
127 * Additional reads
128 * Algorithm
129 * Parameters
130
131 If the user elects to output a MEGAN summary file, an additional text file that includes the following information (among
132 other items) is produced.
133
134 * Creator
135 * Creation date
136 * Content type
137 * Blast mode
138 * Uids
139
140 </help>
141 <expand macro="citations"/>
142 </tool>
143