Mercurial > repos > iuc > obi_tab

annotate obitab.xml @ 4:4cf47c504672 draft default tip

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/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:17:50 +0000
parents 5f7003111e32
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
1 <tool id="obi_tab" name="obitab" version="@TOOL_VERSION@" profile="@PROFILE@">
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
2 <description>converts sequence file to a tabular file</description>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
3 <macros>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
4 <import>macros.xml</import>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
5 </macros>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
6 <expand macro="bio_tools"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
7 <expand macro="requirements"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
8 <expand macro="stdio"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
9 <command><![CDATA[
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
10 @GUNZIP_INPUT@
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
11
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
12 obitab
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
13 --without-progress-bar
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
14 #if $additional_file
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
15 --omit-attribute='$additional_file'
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
16 #end if
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
17 ${output_seq_option}
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
18 ${no_definition_option}
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
19 @INPUT_FORMAT@
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
20 input > '$output'
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
21 ]]></command>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
22 <inputs>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
23 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
24 <param name="output_seq_option" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Do you want to add an extra column?" help="Use this option if you want to add an extra column at the end of the table for the sequence itself"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
25 <param name="no_definition_option" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Do you want to remove column containing the sequence definition?" help="Use this option if you want to remove column containing the sequence definition in the output tab file"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
26 <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
27 <expand macro="input_format_options_macro"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
28 </inputs>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
29 <outputs>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
30 <data format="tabular" name="output"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
31 </outputs>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
32 <tests>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
33 <test expect_num_outputs="1">
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
34 <param name="input" value="output_obisort.fastq" />
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
35 <param name="output_seq_option" value="False"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
36 <param name="no_definition_option" value="True"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
37 <output name="output" file="output_obitab.txt" ftype="tabular"/>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
38 </test>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
39 </tests>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
40 <help><![CDATA[
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
41
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
42
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
43 .. class:: infomark
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
44
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
45 **What it does**
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
46
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
47 obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
48
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
49 @OBITOOLS_LINK@
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
50
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
51 ]]>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
52 </help>
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
53 <expand macro="citation" />
4cf47c504672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
54 </tool>