Mercurial > repos > mvdbeek > add_input_name_as_column

annotate add_input_name_as_column.xml @ 2:ea4ad41e01fc 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/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
author iuc
date Wed, 25 Mar 2020 11:09:05 +0000
parents 07d2cbf43b51
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
1 <tool id="addName" name="Add input name as column" version="0.2.0" profile="17.09">
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
2 <description>to an existing tabular file</description>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
3 <requirements>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
4 <requirement type="package" version="3.7">python</requirement>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
5 </requirements>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
6 <command><![CDATA[
1
07d2cbf43b51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
7 python '$__tool_directory__/'add_input_name_as_column.py
07d2cbf43b51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
8 --input '$input'
07d2cbf43b51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
9 --label '$input.element_identifier'
07d2cbf43b51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
10 --output '$output'
07d2cbf43b51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
11 #if $header.contains_header=="yes":
07d2cbf43b51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
12 --header "$header.colname"
07d2cbf43b51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
13 #end if
2
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
14 $prepend
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
15 ]]></command>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
16 <inputs>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
17 <param format="txt" name="input" type="data" label="to Dataset" help="Dataset missing? See TIP below" />
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
18 <conditional name="header">
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
19 <param name="contains_header" type="select" label="input contains a header line?" >
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
20 <option value="yes" selected="true">Yes</option>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
21 <option value="no">No</option>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
22 </param>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
23 <when value="yes">
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
24 <param name="colname" type="text" value="sample" help="select a column header to be added in the first line">
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
25 <validator type="empty_field" message="please add a column header"/>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
26 </param>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
27 </when>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
28 <when value="no"/>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
29 </conditional>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
30 <param name="prepend" type="boolean" truevalue="--prepend" falsevalue="" checked="false" label="Prepend the colum" />
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
31 </inputs>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
32 <outputs>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
33 <data name="output" format="tabular" />
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
34 </outputs>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
35 <tests>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
36 <test>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
37 <param name="input" value="signature.tab" ftype="tabular" />
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
38 <param name="contains_header" value="yes" />
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
39 <param name="colname" value="sample" />
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
40 <output name="output" file="signature_with_header.tab" ftype="tabular"/>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
41 </test>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
42 <test>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
43 <param name="input" value="signature.tab" ftype="tabular" />
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
44 <param name="contains_header" value="no" />
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
45 <param name="prepend" value="true" />
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
46 <output name="output" file="signature_without_header.tab" ftype="tabular"/>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
47 </test>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
48 </tests>
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
49 <help><![CDATA[
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
50 **What it does**
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
51
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
52 Adds a new column with the name of the input file as it appears in the history.
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
53 By default the column is appended.
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
54
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
55 -----
0
bfebefdd5ba4 Initial Commit.
mvdbeek
parents:
diff changeset
56
bfebefdd5ba4 Initial Commit.
mvdbeek
parents:
diff changeset
57 .. class:: infomark
bfebefdd5ba4 Initial Commit.
mvdbeek
parents:
diff changeset
58
2
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
59 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
0
bfebefdd5ba4 Initial Commit.
mvdbeek
parents:
diff changeset
60
2
ea4ad41e01fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 1
diff changeset
61 ]]></help>
0
bfebefdd5ba4 Initial Commit.
mvdbeek
parents:
diff changeset
62 </tool>