Mercurial > repos > iuc > megan_daa2info

annotate daa2info.xml @ 0:2f8df8e575f2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
1 <tool id="megan_daa2info" name="MEGAN: Get information" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
2 <description>about a DIAMOND file</description>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
3 <macros>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
5 </macros>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
6 <expand macro="bio_tools"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
9 #set input_identifier = 'input.' + $input.ext.upper()
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
10 ln -s '${input}' '${input_identifier}' &&
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
11
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
12 daa2info
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
13 --in '${input_identifier}'
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
14 #if str($input_is_meganized_cond.input_is_meganized) == 'yes':
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
15 --listMore
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
16 #if str($input_is_meganized_cond.list_class2count_cond.list_class2count) == 'yes':
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
17 --class2count '$input_is_meganized_cond.list_class2count_cond.class2count'
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
18 $input_is_meganized_cond.list_class2count_cond.sum
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
19 #end if
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
20 #if str($input_is_meganized_cond.list_read2class_cond.list_read2class) == 'yes':
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
21 --read2class '$input_is_meganized_cond.list_read2class_cond.read2class'
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
22 #end if
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
23 $input_is_meganized_cond.names
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
24 $input_is_meganized_cond.paths
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
25 $input_is_meganized_cond.prefixRank
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
26 $input_is_meganized_cond.majorRanksOnly
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
27 #if str($input_is_meganized_cond.bo_or_vo) != 'do_not_restrict':
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
28 $input_is_meganized_cond.bo_or_vo
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
29 #end if
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
30 $input_is_meganized_cond.ignoreUnassigned
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
31 #else:
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
32 --list
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
33 #end if
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
34 #if $extractSummaryFile:
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
35 --extractSummaryFile '$output_summary'
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
36 #end if
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
37 --out '${output}'
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
38 ]]></command>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
39 <inputs>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
40 <param name="input" argument="--in" type="data" format="daa" label="Input DIAMOND file"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
41 <conditional name="input_is_meganized_cond">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
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">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
43 <option value="no" selected="true">No</option>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
44 <option value="yes">Yes</option>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
45 </param>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
46 <when value="no"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
47 <when value="yes">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
48 <conditional name="list_class2count_cond">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
49 <param name="list_class2count" type="select" label="List class to count for named classification(s)?">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
50 <option value="no" selected="true">No</option>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
51 <option value="yes">Yes</option>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
52 </param>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
53 <when value="no"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
54 <when value="yes">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
55 <param argument="--class2count" type="select" label="Select class to count for named classification(s)">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
56 <expand macro="classification_options"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
57 </param>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
58 <param argument="--sum" type="boolean" truevalue="--sum" falsevalue="" checked="false" label="Use summarized rather than assigned counts when listing class to count?"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
59 </when>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
60 </conditional>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
61 <conditional name="list_read2class_cond">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
62 <param name="list_read2class" type="boolean" truevalue="true" falsevalue="false" checked="false" label="List read to class assignments for named classification(s)?"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
63 <when value="false"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
64 <when value="true">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
65 <param argument="--read2class" type="select" label="Select read to class assignments for named classification(s)">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
66 <expand macro="classification_options"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
67 </param>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
68 </when>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
69 </conditional>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
70 <param argument="--names" type="boolean" truevalue="--names" falsevalue="" checked="false" label="Report class names rather than class Id numbers?"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
71 <param argument="--paths" type="boolean" truevalue="--paths" falsevalue="" checked="false" label="Report class paths rather than class Id numbers?"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
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?"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
73 <param argument="--majorRanksOnly" type="boolean" truevalue="--majorRanksOnly" falsevalue="" checked="false" label="Only use major taxonomic ranks?"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
74 <param name="bo_or_vo" type="select" label="Restrict reporting to either bacterial reads or viral reads in taxonomic report">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
75 <option value="do_not_restrict" selected="true">Do not restrict</option>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
76 <option value="--bacteriaOnly" selected="true">Bacterial reads and counts</option>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
77 <option value="--virusOnly">Viral reads and counts</option>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
78 </param>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
79 <param argument="--ignoreUnassigned" type="boolean" truevalue="--ignoreUnassigned" falsevalue="" checked="true" label="Don't report on reads that are unassigned?"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
80 </when>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
81 </conditional>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
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"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
83 </inputs>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
84 <outputs>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
85 <data name="output" format="txt"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
86 <data name="output_summary" format="txt" label="${tool.name} on ${on_string} (MEGAN summary)">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
87 <filter>extractSummaryFile</filter>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
88 </data>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
89 </outputs>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
90 <tests>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
91 <test expect_num_outputs="1">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
92 <param name="input" value="input.daa" ftype="daa"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
93 <output name="output" file="daa2info_output1.txt" ftype="txt" compare="contains"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
94 </test>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
95 <test expect_num_outputs="1">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
96 <param name="input" value="input_meganized.daa" ftype="daa"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
97 <param name="input_is_meganized" value="yes"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
98 <output name="output" file="daa2info_output2.txt" ftype="txt" compare="contains"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
99 </test>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
100 <test expect_num_outputs="2">
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
101 <param name="input" value="input_meganized.daa" ftype="daa"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
102 <param name="input_is_meganized" value="yes"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
103 <param name="bo_or_vo" value="--virusOnly"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
104 <param name="extractSummaryFile" value="true"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
105 <output name="output" file="daa2info_output2.txt" ftype="txt" compare="contains"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
106 <output name="output_summary" file="daa2info_output_summary2.txt" ftype="txt" compare="contains"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
107 </test>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
108 </tests>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
109 <help>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
110 **What it does**
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
111
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
112 Analyses a DIAMOND (i.e., a Direct Access Archive or DAA) file, a proprietary file format developed by PowerISO Computing
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
113 for disk image files, and outputs a text file containing information about the file. The information includes the following.
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
114
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
115 * Number of reads
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
116 * Alignment mode
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
117 * Whether the file is meganized
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
118 * Classifications
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
119
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
120 If the DIAMOND file is meganized (i.e., it was produced by the MEGAN: DAA Meganizer tool), a summary that includes the
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
121 following information (among other items) is included in the output.
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
122
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
123 * Content type
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
124 * Names
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
125 * Uids
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
126 * Sizes
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
127 * Additional reads
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
128 * Algorithm
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
129 * Parameters
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
130
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
131 If the user elects to output a MEGAN summary file, an additional text file that includes the following information (among
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
132 other items) is produced.
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
133
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
134 * Creator
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
135 * Creation date
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
136 * Content type
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
137 * Blast mode
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
138 * Uids
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
139
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
140 </help>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
141 <expand macro="citations"/>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
142 </tool>
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
143